U.S. patent application number 14/193835 was filed with the patent office on 2015-09-03 for levels of cxcl 10/ip-10 forms and soluble cd26/dppiv activity as early predictive biomarkers for hiv/siv associated mucosal inflammation and progression towards aids.
This patent application is currently assigned to Institut Pasteur. The applicant listed for this patent is Institut Pasteur. Invention is credited to Matthew Albert, Cecile Goujard, Yoann Madec, Laurence Meyer, Michaela MULLER-TRUTWIN, Michael Ploquin.
Application Number | 20150247853 14/193835 |
Document ID | / |
Family ID | 54006662 |
Filed Date | 2015-09-03 |
United States Patent
Application |
20150247853 |
Kind Code |
A1 |
MULLER-TRUTWIN; Michaela ;
et al. |
September 3, 2015 |
LEVELS OF CXCL 10/IP-10 FORMS AND SOLUBLE CD26/DPPIV ACTIVITY AS
EARLY PREDICTIVE BIOMARKERS FOR HIV/SIV ASSOCIATED MUCOSAL
INFLAMMATION AND PROGRESSION TOWARDS AIDS
Abstract
The invention provides methods for the identification of
patients capable of controlling HIV progression, as well as to the
identification of an antagonist form of IP-10 associated to HIV
progression control and the uses thereof for improving the
immunological response of HIV patients.
Inventors: |
MULLER-TRUTWIN; Michaela;
(Paris, FR) ; Ploquin; Michael; (Paris, FR)
; Albert; Matthew; (Paris, FR) ; Madec; Yoann;
(Paris, FR) ; Goujard; Cecile; (Paris, FR)
; Meyer; Laurence; (Paris, FR) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Institut Pasteur |
Paris |
|
FR |
|
|
Assignee: |
Institut Pasteur
Paris
FR
|
Family ID: |
54006662 |
Appl. No.: |
14/193835 |
Filed: |
February 28, 2014 |
Current U.S.
Class: |
435/5 |
Current CPC
Class: |
G01N 2800/52 20130101;
G01N 33/56988 20130101; G01N 2800/50 20130101; G01N 2333/522
20130101; G01N 2333/70596 20130101 |
International
Class: |
G01N 33/569 20060101
G01N033/569 |
Claims
1. A method of determining the likelihood that a subject identified
as being infected with HIV will develop AIDS, said method
comprising the steps of: a) measuring the sIP-10 level in a sample
of the said subject; and b) determining the likelihood that said
subject will develop AIDS based on said level.
2. The method of claim 1, further comprising a prior step of
obtaining said sample.
3. The method of claim 1, wherein said sample is selected from the
group of blood, plasma, lymph, bone marrow fluid, pleural fluid,
peritoneal fluid, spinal fluid, abdominal fluid, pancreatic fluid,
cerebrospinal fluid, brain fluid, ascites, urine, saliva, bronchial
lavage, bile, sweat, tears, ear flow, sputum, semen, vaginal flow,
milk, amniotic fluid, or secretions of respiratory, intestinal or
genitourinary tract.
4. The method of claim 1, wherein said sIP-10 level is measured by
a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
5. The method of claim 1, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
6. A method for selecting an anti-HIV therapy for a subject
identified as being infected with HIV, said method comprising the
steps of: a) measuring the sIP-10 level in a sample of the said
subject; b) determining the likelihood that said subject will
develop AIDS based on said level; and c) selecting the therapy
based on said likelihood.
7. The method of claim 6, further comprising a prior step of
obtaining said sample.
8. The method of claim 6, wherein said sample is selected from the
group of blood, plasma, lymph, bone marrow fluid, pleural fluid,
peritoneal fluid, spinal fluid, abdominal fluid, pancreatic fluid,
cerebrospinal fluid, brain fluid, ascites, urine, saliva, bronchial
lavage, bile, sweat, tears, ear flow, sputum, semen, vaginal flow,
milk, amniotic fluid, or secretions of respiratory, intestinal or
genitourinary tract.
9. The method of claim 6, wherein said sIP-10 level is measured by
a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
10. The method of claim 6, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
11. The method of claim 6, wherein the therapy is selected from the
group consisting of: highly active antiretroviral therapy (HAART),
protease inhibitors, fusion inhibitors, integrase inhibitors,
co-receptor specific agents, 3TC, AZT, nevirapine, non-nucleoside
analogue reverse transcriptase inhibitors, nucleoside analogue
reverse transcriptase inhibitors and vaccine therapy.
12. A method of determining the prognosis of a subject identified
as being infected with HIV, said method comprising the steps of: c)
measuring the sIP-10 level in a sample of the said subject; and d)
determining the prognosis that said subject based on said
level.
13. The method of claim 12, further comprising a prior step of
obtaining said sample.
14. The method of claim 12, wherein said sample is selected from
the group of blood, plasma, lymph, bone marrow fluid, pleural
fluid, peritoneal fluid, spinal fluid, abdominal fluid, pancreatic
fluid, cerebrospinal fluid, brain fluid, ascites, urine, saliva,
bronchial lavage, bile, sweat, tears, ear flow, sputum, semen,
vaginal flow, milk, amniotic fluid, or secretions of respiratory,
intestinal or genitourinary tract.
15. The method of claim 12, wherein said sIP-10 level is measured
by a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
16. The method of claim 12, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
17. A method for selecting an anti-HIV therapy for a subject
identified as being infected with HIV, said method comprising the
steps of: a) measuring the sIP-10 level in a sample of the said
subject; b) determining the prognosis of said subject based on said
level; and c) selecting the therapy based on said prognosis.
18. The method of claim 17, further comprising a prior step of
obtaining said sample.
19. The method of claim 17, wherein said sample is selected from
the group of blood, plasma, lymph, bone marrow fluid, pleural
fluid, peritoneal fluid, spinal fluid, abdominal fluid, pancreatic
fluid, cerebrospinal fluid, brain fluid, ascites, urine, saliva,
bronchial lavage, bile, sweat, tears, ear flow, sputum, semen,
vaginal flow, milk, amniotic fluid, or secretions of respiratory,
intestinal or genitourinary tract.
20. The method of claim 17, wherein said sIP-10 level is measured
by a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
21. The method of claim 17, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
22. The method of claim 17, wherein the subject has above 500
cells/.mu.L.
23. The method of claim 17, wherein the therapy is selected from
the group consisting of: highly active antiretroviral therapy
(HAART), protease inhibitors, fusion inhibitors, integrase
inhibitors, co-receptor specific agents, 3TC, AZT, nevirapine,
non-nucleoside analogue reverse transcriptase inhibitors,
nucleoside analogue reverse transcriptase inhibitors and vaccine
therapy.
24. A method of determining the likelihood that a subject
identified as being infected with HIV will develop AIDS, said
method comprising the steps of: a) measuring the sIP-10 level in a
sample of the said subject; b) measuring the total IP-10 level in
said sample of the said subject; c) calculating the ratio of sIP-10
to total IP-10; and d) determining the likelihood that said subject
will develop AIDS based on said ratio.
25. The method of claim 24, further comprising a prior step of
obtaining said sample.
26. The method of claim 24, wherein said sample is selected from
the group of blood, plasma, lymph, bone marrow fluid, pleural
fluid, peritoneal fluid, spinal fluid, abdominal fluid, pancreatic
fluid, cerebrospinal fluid, brain fluid, ascites, urine, saliva,
bronchial lavage, bile, sweat, tears, ear flow, sputum, semen,
vaginal flow, milk, amniotic fluid, or secretions of respiratory,
intestinal or genitourinary tract.
27. The method of claim 24, wherein said sIP-10 level is measured
by a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
28. The method of claim 24, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
29. A method for selecting an anti-HIV therapy for a subject
identified as being infected with HIV, said method comprising the
steps of: a) measuring the sIP-10 level in a sample of the said
subject; b) measuring the total IP-10 level in said sample of the
said subject; d) calculating the ratio of sIP-10 to total IP-10; e)
determining the likelihood that said subject will develop AIDS
based on said ratio; and f) selecting the therapy based on said
likelihood.
30. The method of claim 29, further comprising a prior step of
obtaining said sample.
31. The method of claim 29, wherein said sample is selected from
the group of blood, plasma, lymph, bone marrow fluid, pleural
fluid, peritoneal fluid, spinal fluid, abdominal fluid, pancreatic
fluid, cerebrospinal fluid, brain fluid, ascites, urine, saliva,
bronchial lavage, bile, sweat, tears, ear flow, sputum, semen,
vaginal flow, milk, amniotic fluid, or secretions of respiratory,
intestinal or genitourinary tract.
32. The method of claim 29, wherein said sIP-10 level is measured
by a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
33. The method of claim 29, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
34. The method of claim 29, wherein the therapy is selected from
the group consisting of: highly active antiretroviral therapy
(HAART), protease inhibitors, fusion inhibitors, integrase
inhibitors, co-receptor specific agents, 3TC, AZT, nevirapine,
non-nucleoside analogue reverse transcriptase inhibitors,
nucleoside analogue reverse transcriptase inhibitors and vaccine
therapy.
35. A method of determining the prognosis of a subject identified
as being infected with HIV, said method comprising the steps of: a)
measuring the sIP-10 level in a sample of the said subject; b)
measuring the total IP-10 level in said sample of the said subject;
c) calculating the ratio of sIP-10 to total IP-10; and d)
determining the prognosis that said subject based on said
ratio.
36. The method of claim 35, further comprising a prior step of
obtaining said sample.
37. The method of claim 35, wherein said sample is selected from
the group of blood, plasma, lymph, bone marrow fluid, pleural
fluid, peritoneal fluid, spinal fluid, abdominal fluid, pancreatic
fluid, cerebrospinal fluid, brain fluid, ascites, urine, saliva,
bronchial lavage, bile, sweat, tears, ear flow, sputum, semen,
vaginal flow, milk, amniotic fluid, or secretions of respiratory,
intestinal or genitourinary tract.
38. The method of claim 35, wherein said sIP-10 level is measured
by a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
39. The method of claim 35, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
40. A method for selecting an anti-HIV therapy for a subject
identified as being infected with HIV, said method comprising the
steps of: a) measuring the sIP-10 level in a sample of the said
subject; b) measuring the total IP-10 level in said sample of the
said subject; c) calculating the ratio of sIP-10 to total IP-10; d)
determining the prognosis of said subject based on said ratio; and
e) selecting the therapy based on said prognosis.
41. The method of claim 40, further comprising a prior step of
obtaining said sample.
42. The method of claim 40, wherein said sample is selected from
the group of blood, plasma, lymph, bone marrow fluid, pleural
fluid, peritoneal fluid, spinal fluid, abdominal fluid, pancreatic
fluid, cerebrospinal fluid, brain fluid, ascites, urine, saliva,
bronchial lavage, bile, sweat, tears, ear flow, sputum, semen,
vaginal flow, milk, amniotic fluid, or secretions of respiratory,
intestinal or genitourinary tract.
43. The method of claim 40, wherein said sIP-10 level is measured
by a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
44. The method of claim 40, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
45. The method of claim 40, wherein the therapy is selected from
the group consisting of: highly active antiretroviral therapy
(HAART), protease inhibitors, fusion inhibitors, integrase
inhibitors, co-receptor specific agents, 3TC, AZT, nevirapine,
non-nucleoside analogue reverse transcriptase inhibitors,
nucleoside analogue reverse transcriptase inhibitors and vaccine
therapy.
46. A method of determining the likelihood that a subject
identified as being infected with HIV will develop AIDS, said
method comprising the steps of: a) measuring the soluble DPPIV
activity in a sample of the said subject; and b) determining the
likelihood that said subject will develop AIDS based on said
activity.
47. The method of claim 46, further comprising a prior step of
obtaining said sample.
48. The method of claim 46, wherein said sample is selected from
the group of blood, plasma, lymph, bone marrow fluid, pleural
fluid, peritoneal fluid, spinal fluid, abdominal fluid, pancreatic
fluid, cerebrospinal fluid, brain fluid, ascites, urine, saliva,
bronchial lavage, bile, sweat, tears, ear flow, sputum, semen,
vaginal flow, milk, amniotic fluid, or secretions of respiratory,
intestinal or genitourinary tract.
49. The method of claim 46, wherein said sIP-10 level is measured
by a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
50. The method of claim 46, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
51. A method for selecting an anti-HIV therapy for a subject
identified as being infected with HIV, said method comprising the
steps of: a) measuring the soluble DPPIV activity in a sample of
the said subject; b) determining the likelihood that said subject
will develop AIDS based on said activity; and c) selecting the
therapy based on said likelihood.
52. The method of claim 51, further comprising a prior step of
obtaining said sample.
53. The method of claim 51, wherein said sample is selected from
the group of blood, plasma, lymph, bone marrow fluid, pleural
fluid, peritoneal fluid, spinal fluid, abdominal fluid, pancreatic
fluid, cerebrospinal fluid, brain fluid, ascites, urine, saliva,
bronchial lavage, bile, sweat, tears, ear flow, sputum, semen,
vaginal flow, milk, amniotic fluid, or secretions of respiratory,
intestinal or genitourinary tract.
54. The method of claim 51, wherein said sIP-10 level is measured
by a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
55. The method of claim 51, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
56. The method of claim 51, wherein the therapy is selected from
the group consisting of: highly active antiretroviral therapy
(HAART), protease inhibitors, fusion inhibitors, integrase
inhibitors, co-receptor specific agents, 3TC, AZT, nevirapine,
non-nucleoside analogue reverse transcriptase inhibitors,
nucleoside analogue reverse transcriptase inhibitors and vaccine
therapy.
57. A method of determining the prognosis of a subject identified
as being infected with HIV, said method comprising the steps of: a)
measuring the soluble DPPIV activity in a sample of the said
subject; and b) determining the prognosis that said subject based
on said activity.
58. The method of claim 57, further comprising a prior step of
obtaining said sample.
59. The method of claim 57, wherein said sample is selected from
the group of blood, plasma, lymph, bone marrow fluid, pleural
fluid, peritoneal fluid, spinal fluid, abdominal fluid, pancreatic
fluid, cerebrospinal fluid, brain fluid, ascites, urine, saliva,
bronchial lavage, bile, sweat, tears, ear flow, sputum, semen,
vaginal flow, milk, amniotic fluid, or secretions of respiratory,
intestinal or genitourinary tract.
60. The method of claim 57, wherein said sIP-10 level is measured
by a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
61. The method of claim 57, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
62. A method for selecting an anti-HIV therapy for a subject
identified as being infected with HIV, said method comprising the
steps of: a) measuring the soluble DPPIV activity in a sample of
the said subject; b) determining the prognosis of said subject
based on said activity; and c) selecting the therapy based on said
prognosis.
63. The method of claim 62, further comprising a prior step of
obtaining said sample.
64. The method of claim 62, wherein said sample is selected from
the group of blood, plasma, lymph, bone marrow fluid, pleural
fluid, peritoneal fluid, spinal fluid, abdominal fluid, pancreatic
fluid, cerebrospinal fluid, brain fluid, ascites, urine, saliva,
bronchial lavage, bile, sweat, tears, ear flow, sputum, semen,
vaginal flow, milk, amniotic fluid, or secretions of respiratory,
intestinal or genitourinary tract.
65. The method of claim 62, wherein said sIP-10 level is measured
by a method selected from the group of western-blot analysis, ELISA
assays, immuno-reactivity assays, and column assays using
fluorescence, antibodies and radiolabeled markers.
66. The method of claim 62, wherein the subject is selected in the
group of subjects having T cell counts of less than 200
cells/.mu.L, comprised between 200 and 500 cells/.mu.L, and above
500 cells/.mu.L.
67. The method of claim 62, wherein the therapy is selected from
the group consisting of: highly active antiretroviral therapy
(HAART), protease inhibitors, fusion inhibitors, integrase
inhibitors, co-receptor specific agents, 3TC, AZT, nevirapine,
non-nucleoside analogue reverse transcriptase inhibitors,
nucleoside analogue reverse transcriptase inhibitors and vaccine
therapy.
Description
FIELD OF THE INVENTION
[0001] The invention relates to the field of immunology and, in
particular, to methods for the identification of patients capable
of controlling HIV progression, as well as to the identification of
an antagonist form of IP-10 associated to HIV progression control
and the uses thereof for improving the immunological response of
HIV patients.
BACKGROUND OF THE INVENTION
[0002] HIV disease is a continuum of progressive damage to the
immune system from the time of infection to the manifestation of
severe immunologic damage by opportunistic infections, neoplasms,
wasting, or low CD4 lymphocyte count that define AIDS. In the
absence of antiretroviral therapy, this results in an important
immunologic impairment with the consequent appearance of
opportunistic infections and, lastly, death. The time it takes to
traverse this spectrum varies greatly, ranging from 1 year or less
in some persons to a still unknown upper limit in others that has
reached nearly 20 years in a few individuals.
[0003] Significant advances in antiretroviral therapy of HIV
infection have been made since the introduction of zidovudine (AZT)
in 1987. Intensive research on HIV led to the development of highly
active antiretroviral therapies (HAART). HAART is defined as
treatment with at least three active anti-retroviral medications,
commonly reverse transcriptase inhibitors and protease inhibitors.
These therapies have been extremely successful in controlling the
spread of the disease. Indeed, with the advent of HAART, HIV
infection is now manageable as a chronic disease in patients who
have access to medication and who achieve durable virological
suppression.
[0004] However, residual chronic inflammation persists in
HAART-treated patients and is associated with increased risk of
cardiovascular diseases and mortality. Both AIDS and non-AIDS
mortality are attributed to chronic inflammation in HIV-infected
individuals. No therapeutic strategy exists to reduce this
inflammation efficiently. This is in part explained by the fact
that the inflammatory pathways involved are not well identified.
Chronic immune activation is considered as the major driving force
for CD4.sup.+ T cell depletion and progression towards AIDS in
HIV-infected individuals. HIV-triggered chronic inflammation
remains higher even in patients who control viral load (patients
under efficient anti-retroviral treatment and HIV controllers in
comparison to healthy donors. Current antiretroviral treatments are
highly efficient, but fail to abolish residual chronic immune
activation.
[0005] There is thus an urgent need to understand the factors,
which drive this inflammation and to define good surrogate markers
for this inflammation.
BRIEF SUMMARY OF THE INVENTION
[0006] The present disclosure is related to the discovery that
levels of certain biomarkers, including the short form of IP-10
(sIP-10), in the plasma of HIV patients are negative predictors of
those patients who will progress towards AIDS.
[0007] Accordingly, in one aspect of the invention, a method is
provided for assessing the likelihood of a patient to develop AIDS.
Generally, the method includes at least the following steps: (1)
assaying a biological sample from a patient identified as infected
with HIV to determine the level of sIP-10 in the biological sample;
and (2) assessing the likelihood that the patient will develop AIDS
based on the level of sIP-10.
[0008] In another aspect of the invention, a method is provided for
prognosing of a patient identified as suffering from HIV infection.
Generally, the method includes at least the following steps: (1)
determining the level of sIP-10 in a biological sample taken from
the patient; and (2) determining the prognosis of the patient based
on the level of sIP-10.
[0009] In another aspect of the invention, a method is provided for
treating HIV infection. Generally, the method includes at least the
following steps: (1) obtaining a biological sample from a patient
identified as having HIV infection; (2) determining the level of
sIP-10 in the biological sample; and (3) selecting a drug therapy
based on the level of sIP-10 in the sample.
[0010] More precisely, the present disclosure is related to the
discovery that the relative levels of sIP-10 are negative
predictors of those patients who will progress towards AIDS.
[0011] Accordingly, in one aspect of the invention, a method is
provided for assessing the likelihood of a patient to develop AIDS.
Generally, the method includes at least the following steps: (1)
assaying a biological sample from a patient identified as infected
with HIV to determine the level of sIP-10 in the biological sample;
(2) determining the ratio of sIP-10 to total IP-10, and (3)
assessing the likelihood that the patient will develop AIDS based
on the ratio of sIP-10 to total IP-10.
[0012] In another aspect of the invention, a method is provided for
prognosing of a patient identified as suffering from HIV infection.
Generally, the method includes at least the following steps: (1)
determining the level of sIP-10 in a biological sample taken from
the patient; (2) determining the ratio of sIP-10 to total IP-10 in
said biological sample, and (3) determining the prognosis of the
patient based on the ratio of sIP-10 to total IP-10.
[0013] In another aspect of the invention, a method is provided for
treating HIV infection. Generally, the method includes at least the
following steps: (1) obtaining a biological sample from a patient
identified as having HIV infection; (2) determining the level of
sIP-10 in the biological sample; (3) determining the ratio of
sIP-10 to total IP-10 in the biological sample, and (4) selecting a
drug therapy based on the ratio of sIP-10 to total IP-10 in the
sample.
[0014] The present disclosure is also related to the discovery that
the enzymatic activities of certain biomarkers, including the
dipeptidylpeptidase IV enzyme (DPPIV), in the plasma of HCV
patients are negative predictors of those patients who will
progress towards AIDS.
[0015] Accordingly, in one aspect of the invention, a method is
provided for assessing the likelihood of a patient to develop AIDS.
Generally, the method includes at least the following steps: (1)
assaying a biological sample from a patient identified as infected
with HIV to determine the activity of DPPIV in the biological
sample; and (2) assessing the likelihood that the patient will
develop AIDS based on the activity of DPPIV.
[0016] In another aspect of the invention, a method is provided for
prognosing of a patient identified as suffering from HIV infection.
Generally, the method includes at least the following steps: (1)
determining the activity of DPPIV in a biological sample taken from
the patient; and (2) determining the prognosis of the patient based
on the activity of DPPIV.
[0017] In another aspect of the invention, a method is provided for
treating HIV infection. Generally, the method includes at least the
following steps: (1) obtaining a biological sample from a patient
identified as having HIV infection; (2) determining the activity of
DPPIV in the biological sample; and (3) selecting a drug therapy
based on the activity of DPPIV in the sample.
[0018] All methods and materials similar or equivalent to those
described herein can be used in the practice or testing of the
present invention, with suitable methods and materials being
described herein. The practice of the invention employs, unless
other otherwise indicated, conventional techniques or protein
chemistry, molecular virology, microbiology, recombinant DNA
technology, and pharmacology, which are within the skill of the
art. Such techniques are explained fully in the literature (see
e.g., Ausubel et al., Short Protocols in Molecular Biology, Current
Protocols; 5th Ed., 2002; Remington's Pharmaceutical Sciences, 17th
ed., Mack Publishing Co., Easton, Pa., 1985; and Sambrook et al.,
Molecular Cloning: A Laboratory Manual, Cold Spring Harbor
Laboratory Press; 3rd Ed., 2001). The nomenclatures used in
connection with, and the laboratory procedures and techniques of,
molecular and cellular biology, protein biochemistry, enzymology
and medicinal and pharmaceutical chemistry described herein are
those well-known and commonly used in the art. All publications,
patent applications, patents, and other references mentioned herein
are incorporated by reference in their entirety. Further, the
materials, methods, and examples are illustrative only and are not
intended to be limiting, unless otherwise specified.
[0019] Other features and advantages of the invention will be
apparent from the following detailed description, and from the
claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0020] FIG. 1: Controlled CXCL10/IP-10 expression in non-pathogenic
SIV infection. A. IP-10 gene expression levels in enriched lymph
node CD4+ cells are shown here as heatmap. Gene expression levels
were assessed using microarrays at different time points before and
after SIVagm and SIVmac infection in AGM and MAC, respectively. B.
IP-10 expression levels in plasma before and after SIVagm and
SIVmac infection are represented here. Levels were quantified using
a commercial ELISA (R&D) as described in (Liovat et al., PLoS
One, 7(10): e46143, 2012). Median from 12 AGM is displayed along
with levels obtained in 3 MAC with a rapid disease progression
profile or with 2 MAC with a slow disease progression profile. In
addition data are shown also as a fold change of levels measured at
day 65 p.i. against median of values assessed before infection for
each animal. S=MAC slow progressor, P=MAC progressor and R=MAC
rapid progressor.
[0021] FIG. 2: IP-10 robustness of prediction for rapid disease
progression. Multivariate regression analysis. Only IP-10 was
significant in the multivariate analysis for prediction of rapid
disease progression, while CD4.sup.+ T cell counts, plasma viral
RNA and cellular viral DNA levels were not.
[0022] FIG. 3: Decreased levels of plasma IP-10 antagonist form and
sDPPIV-like activity during acute infection in HIV-1 infected
individuals progressing rapidly to disease. Frozen plasmas
collected on EDTA were obtained from 134 HIV. patients during
primary infection (Fiebig stage III-IV) of the ANRS Primo Cohort
Co6, and described in (Liovat et al., PLoS One, 7(10): e46143,
2012). Plasma IP-10 antagonist form (short) is presented as a ratio
short (antagonist form): total IP-10. Total IP10 concentrations
were previously measured (Liovat et al., PLoS One, 7(10): e46143,
2012). We also monitored the bioactive sDPPIV titers in plasma,
determined with a luminescence-based assay (Promega). Mann-Whitney
test was used to compare groups of patients. Preliminary data from
53 patients are shown: HIV neg (n=5-16), slow progressors (SP,
n=11), progressors (P, n=17), rapid progressors (RP, n=25).
[0023] FIG. 4: Dynamics of plasma total IP-10 and sDPPIV-like
activity after seroconversion in HIV-1 infected individuals. Frozen
sera collected on EDTA were obtained from 134 HIV.sup.+ patients at
3 (M3), 6 (M6) or 9 (M9) months post alleged date of seroconversion
or even before infection (Pre). Patients were enrolled in the
Amsterdam cohort Studies on HIV/AIDS. Total IP10 concentrations
were measured as previously described (Liovat et al., PLoS One,
7(10): e46143, 2012). We also monitored the bioactive sDPPIV titers
in plasma, determined with a luminescence-based assay (Promega).
Wilcoxon signed rank test was used to compare time points.
[0024] FIG. 5: IP-10 and DPPIV gene expression levels in the gut of
SIV-infected MAC and AGM. We sampled gut tissue at the time point
of euthanasia in SIVmac-infected MAC (n=6) and SIVagm-infected AGM
(n=5) used in other research projects. These necropsies were
performed at day 65 p.i., when inflammatory profiles are already
distinct between MAC and AGM. We harvested fragments of jejunum,
ileum, colon and rectum. Gut intra-epithelial cells (IEC) and gut
mucosal CD4.sup.+ and CD4.sup.neg cells were enriched after
collagenase digestion, centrifugation on a Percoll gradient
followed by a CD4 enrichment using magnetic beads. Gene transcript
expression was determined by RT-PCR using Taqman gene expression
assays. Relative expressions were normalized first against 18sRNA.
On the top panel, Mann-Whitney test and Wilcoxon signed-rank test
were used to compare compartments between species or within each
species, respectively. On bottom panel, correlations were
determined using the Spearman test on normalized values obtained in
the specified cell compartment enriched from the high intestine
(jejunum/Ileum) of each animal against values obtained in the
specified cell compartment enriched from the rectum of each
animal.
[0025] FIG. 6: IP-10 and DPPIV gene expression levels in gut
mucosal CD4+ cells correlate with dynamics of IP-10 and DPPIV in
the blood of SIV-infected MAC and AGM. Plasma total IP-10 and
soluble DPPIV activity were measured as described in previous
figure legends at day 65 post-SIV infection of MAC and AGM. Values
were normalized against values (median) obtained in plasma samples
of the same animals before infection and were expressed as fold
change to baseline (FC o baseline). We searched for any correlation
between those plasma dynamics with the gene expression levels in
the gut mucosal CD4.sup.+ compartment. Each individual dot
represents paired values for each studied animal.
DETAILED DESCRIPTION OF THE INVENTION
Definitions
[0026] Unless specifically defined, all technical and scientific
terms used herein have the same meaning as commonly understood by a
skill artisan in chemistry, biochemistry, cellular biology,
molecular biology, and medical sciences.
[0027] The term "AIDS", as used herein, refers to the symptomatic
phase of HIV infection, and includes both Acquired Immune
Deficiency Syndrome (commonly known as AIDS) and "ARC," or
AIDS-Related Complex. See Adler M, et al, Brit. Med. J. 1987; 294:
1145-1147. The immunological and clinical manifestations of AIDS
are known in the art and include, for example, opportunistic
infections and cancers resulting from immune deficiency.
[0028] As used herein, "T-cell" refers to a group of white blood
cells known as T-lymphocytes that play a central role in
cell-mediated immunity. There are several subsets of T cells, each
with a distinct function (i.e. helper, memory, regulatory, natural
killer).
[0029] The term "CD4.sup.+ T cells", as used herein, refers to a
type of T cells that expresses the CD4 marker. Said CD4.sup.+ T
cells are generally treated as having a pre-defined role as helper
T cells within the immune system. "CD4", as used herein, refers to
a cluster of differentiation 4, a glycoprotein expressed on the
surface of T helper cells, monocytes, macrophages, and dendritic
cells. CD4 is a co-receptor that assists the T cell receptor (TCR)
with an antigen-presenting cell. Using its portion that resides
inside the T cell, CD4 amplifies the signal generated by the TCR by
recruiting an enzyme, known as the tyrosine kinase lck, which is
essential for activating many molecules involved in the signaling
cascade of an activated T cell.
[0030] The term "CD8+ T cells", as used herein, refers to a type of
T cell that expresses the CD8 marker. "CD8", as used herein, refers
to cluster of differentiation 8, a transmembrane glycoprotein that
serves as a co-receptor for the T cell receptor (TCR) expressed in
the cytotoxic T cells implicated in the rejection of transplants
and the destruction of tumor and virally infected cells.
[0031] As used herein, "T-cell function" means any activities which
are inherent to a T-cell. T-cell function means any one of cytokine
secretion, (for example, IL-2), proliferation or survival.
[0032] As used herein, "T-cell survival" means, the ability of a
T-cell to persist in a host organism.
[0033] As used herein, "proliferation" refers to a process by which
a cell undergoes mitosis, or increases in number, size or
content.
[0034] The term "controller", as used herein, refers to a HIV
infected subject that exhibits a decrease in HIV viral load after
infection and that maintains said decreased viral load levels over
time. A "controller" also refers to an HIV-1 infected subject who
remains asymptomatic with normal CD4+ T-cell counts and low or
undetectable plasma viral loads despite having never been treated
with antiretroviral medications. HIV controllers are capable of
maintaining very low viral load levels, for example, plasma HIV R A
levels <2000 copies/mL in the absence of antiretroviral therapy,
measured three times over a period spanning at least 12 months. The
features of controllers as defined by the HIV Controller Consortium
are: i) to maintain HIV RNA levels below 2000 copies/mL, ii) no
antiretroviral therapy for 1 year or longer and iii) episodes of
viremia are acceptable as long as they represent the minority of
all available determinations.
[0035] The term "decreased", as used herein, refers to the level of
a HIV disease prognosis marker, e.g. sIP-10, of a subject at least
1-fold (e.g. 1, 2, 3, 4, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90,
100, 1000, 10,000-fold or more) lower than its reference value.
"Decreased", as it refers to the level of a HIV disease prognosis
marker, e.g. sIP-10, of a subject, signifies also at least 5% lower
(e.g. 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%,
50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%), 95%), 99%), or 100%)
than the level in the reference sample or with respect to the
reference value for said prognosis marker.
[0036] As used herein, "diagnosis" or "identifying a subject
having" refers to a process of determining if an individual is
afflicted with a disease or ailment (e.g., HIV). HIV is diagnosed
for example by detecting either the presence of an HIV polypeptide,
HIV nucleic acid, or a marker associated with HIV.
[0037] The term "HIV", as used herein, include HIV-1 and HIV-2 and
SIV. "HIV-1" means the human immunodeficiency virus type-1. HIV-1
includes, but is not limited to, extracellular virus particles and
the forms of HIV-1 associated with HIV-1 infected cells. HIV-1 is
known to comprise at least ten subtypes (A1, A2, A3, A4, B, C, D,
E, PL F2, G, H, J and K). See Taylor B, et al, MEJM 2008; 359(18):
1965-1966. Subtype B has been associated with the HIV epidemic in
homosexual men and intravenous drug users worldwide. Most HIV-1
immunogens, laboratory adapted isolates, reagents and mapped
epitopes belong to subtype B. In sub-Saharan Africa, India, and
China, areas where the incidence of new HIV infections is high,
HIV-1 subtype B accounts for only a small minority of infections,
and subtype HIV-1 C appears to be the most common infecting
subtype. "HIV-2" means the human immunodeficiency virus type-2.
HIV-2 includes, but is not limited to, extracellular virus
particles and the forms of HIV-2 associated with HIV-2 infected
cells. HIV-2 is known to include at least five subtypes (A, B, C,
D, and E). The term "SIV" refers to simian immunodeficiency virus
which is an HIV-like virus that infects monkeys, chimpanzees, and
other nonhuman primates. SIV includes, but is not limited, to
extracellular virus particles and the forms of SIV associated with
SIV infected cells.
[0038] As used herein, a "HIV disease" encompasses basically all
the physiological conditions that are undergone by an individual
who has been infected by a HIV virus, starting from the time of the
virus infection event until the date of the individual's death,
irrespective of whether the individual's death is a direct or
indirect consequence of the virus infection event. It is recalled
that the infection of an individual with a HIV virus causes a
chronic disease state that progressively causes a reduction of the
effectiveness of the immune system and leaves the HIV-infected
individuals susceptible to opportunistic infections and tumors.
Thus, a HIV disease encompasses the primary infection (or acute
infection) time period, the seroconversion time period, the
asymptomatic stage time period, the early- and medium-stage of HIV
symptomatic disease, as well as the late stage of HIV-1 disease
(also called AIDS).
[0039] As used herein, "identifying" as it refers to a subject that
has a condition refers to the process of assessing a subject and
determining that the subject has a condition, for example, is
infected with HIV.
[0040] The term "increased", as used herein, refers to the level of
a HIV disease prognosis marker, e.g. sIP-10, of a subject at least
1-fold (e.g. 1, 2, 3, 4, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90,
100, 1000, 10,000-fold or more) greater than its reference value.
"Increased", as it refers to the level of a HIV disease prognosis
marker, e.g. sIP-10, of a subject, signifies also at least 5%
greater (e.g. 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%,
40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%), 95%), 99%),
or 100%) than the level in the reference sample or with respect to
the reference value for said prognosis marker.
[0041] As intended herein, the "level" of a HIV disease prognosis
marker, e.g. sIP-10, consists of a quantitative value of the said
prognosis marker in a sample, e.g. in a sample collected from an
HIV-infected patient. In some embodiments, the said quantitative
value does not consist of an absolute value that is actually
measured, but rather consists of a final value resulting from the
taking into consideration of a signal to noise ratio occurring with
the assay format used, and/or the taking into consideration of
calibration reference values that are used to increase
reproducibility of the measures of the level of a HIV disease
marker, from assay-to-assay. In some embodiments, the "level" of a
HIV disease prognosis marker, e.g. sIP-10, is expressed as
arbitrary units, since what is important is that the same kind of
arbitrary units are compared (i) from assay-to-assay, or (ii) from
one HIV-infected patient to others, or (iii) from assays performed
at distinct time periods for the same patient, or (iv) between the
HIV prognosis marker level measured in a patients sample and a
predetermined reference value (which may also be termed a "cut-off"
value herein).
[0042] As used herein, "monitoring disease progression" refers to a
process of determining the severity or stage of a disease in an
individual afflicted with the disease or ailment (e.g., HIV).
[0043] As used herein, "prognosis" refers to a process of
predicting the probable course and outcome of a disease in an
individual afflicted with a disease or ailment (e.g., HIV), or the
likelihood of recovery of an individual from a disease (e.g.,
HIV).
[0044] The term "reference value", as used herein, refers to the
expression level of a HIV disease prognosis marker under
consideration (e.g. sIP-10) in a reference sample. A "reference
sample", as used herein, means a sample obtained from subjects,
preferably two or more subjects, known to be free of the disease
or, alternatively, from the general population. The suitable
reference expression levels of HIV disease prognosis marker can be
determined by measuring the expression levels of said HIV disease
prognosis marker in several suitable subjects, and such reference
levels can be adjusted to specific subject populations. The
reference value or reference level can be an absolute value; a
relative value; a value that has an upper or a lower limit; a range
of values; an average value; a median value, a mean value, or a
value as compared to a particular control or baseline value. A
reference value can be based on an individual sample value such as,
for example, a value obtained from a sample from the subject being
tested, but at an earlier point in time. The reference value can be
based on a large number of samples, such as from population of
subjects of the chronological age matched group, or based on a pool
of samples including or excluding the sample to be tested.
[0045] As used herein, the term "biological sample" or "sample"
refers to a whole organism or a subset of its tissues, cells or
component parts (e.g. blood vessel, including artery, vein and
capillary, body fluids, including but not limited to blood, serum,
mucus, lymphatic fluid, synovial fluid, cerebrospinal fluid,
saliva, amniotic fluid, amniotic cord blood, urine, vaginal fluid
and semen). "Biological sample" further refers to a homogenate,
lysate or extract prepared from a whole organism or a subset of its
tissues, cells or component parts, or a fraction or portion
thereof. Lastly, "biological sample" refers to a medium, such as a
nutrient broth or gel in which an organism has been propagated,
which contains cellular components, such as proteins or nucleic
acid molecules.
[0046] As used herein, "selecting" refers to the process of
determining that an identified subject will receive an agent to
treat the occurrence of a condition (e.g., HIV). Selecting can be
based on an individual's susceptibility to a particular disease or
condition due to, for example, family history, lifestyle, age,
ethnicity, or other factors.
[0047] A "subject" which may be subjected to the methodology
described herein may be any of mammalian animals including human,
dog, cat, cattle, goat, pig, swine, sheep and monkey. A human
subject can be known as a patient. In one embodiment, "subject" or
"subject in need" refers to a mammal that is infected with HIV or
is suspected of being infected with HIV or has been diagnosed with
HIV infection. As used herein, an "HIV infected subject" refers to
a mammal that is infected with HIV or has been diagnosed with HIV
infection. A "control subject" refers to a mammal that is not
infected with HIV, and is not suspected of being diagnosed with
HIV.
[0048] As used herein, the terms "treat," treating," "treatment,"
and the like refer to reducing or ameliorating the symptoms of a
disorder (e.g., HIV infection) and/or symptoms associated
therewith. It will be appreciated that, although not precluded,
treating a disorder or condition does not require that the
disorder, condition or symptoms associated therewith be completely
eliminated.
[0049] As used herein "treating" a disease in a subject or
"treating" a subject having a disease refers to subjecting the
subject to a pharmaceutical treatment, e.g., the administration of
a drug, such that the extent of the disease is decreased or
prevented. For example, treating results in the reduction of at
least one sign or symptom of the disease or condition. Treatment
includes (but is not limited to) administration of a composition,
such as a pharmaceutical composition, and may be performed either
prophylactically, or subsequent to the initiation of a pathologic
event. Treatment can require administration of an agent and/or
treatment more than once.
Methods for Prognosing an HIV Disease
[0050] IP-10 is a CXC chemokine (NP.sub.--001556) which functions
to recruit activated and memory lymphocytes to sites of
inflammation. The secreted bioactive form (after cleavage of the
signal peptide) is a polypeptide of 77 residues (positions 22-98 of
NP.sub.--001556; SEQ ID NO: 1), herein designated IP-10, which
binds the CXCR3 receptor. IP-10 also exists in a truncated form,
herein referred to as "short IP-10" or "sIP-10", which is obtained
by the removal of the two N-terminal amino acids of the secreted
bioactive form (amino acids 24-98 of NP.sub.--001556; SEQ ID NO:
2).
[0051] In contrast to native IP-10, sIP-10 is endowed with
antagonist properties and repels activated and memory lymphocytes
from sites of inflammation.
[0052] IP-10 has previously been identified as a negative indicator
for chronic HCV patients receiving the IFN/ribavirin treatment,
i.e. high levels of plasma IP-10 are predictive of the failure to
respond to this therapy. These elevated IP-10 levels are mainly in
the short antagonist form, preventing trafficking of CXCR3.sup.+
lymphocytes capable to control HCV replication, to the liver, thus
diminishing HCV control.
[0053] The present application discloses sIP-10 as a clinically
important negative predictive marker for likelihood to progress
rapidly towards AIDS. The present inventors have found that,
surprisingly, sIP-10 antagonist levels are dramatically reduced
upon HIV infection. Moreover, they were reduced to a higher level
in the rapid progressors than in comparison to slow progressors.
Indeed, the inventors have shown that sIP-10 is a strong negative
predictor of rapid disease progression. Thus, whereas good
prognosis is associated with low levels of sIP-10 during HCV
infection (Liovat et al., PLoS One, 7(10): e46143, 2012), it is
correlated with high sIP-10 levels in the case of HIV infection,
which was unexpected.
[0054] This represents an important and medically useful discovery.
This discovery enables the discrimination of patients, prior to
treatment, into a group of patients that is likely not to develop
clinical AIDS symptoms and a group of patients that will
spontaneously progress towards AIDS and will thus require specific
and targeted therapeutic treatment. Determining that a patient is
likely to remain asymptomatic may save them from expensive
treatment with significant side effects. This diagnostic tool may
also assist physicians in identifying patients who are likely to
progress to AIDS and thus may suggest those patients require
earlier or more aggressive treatment.
[0055] In a first aspect, the present invention relates to a method
of determining the likelihood that a subject identified as being
infected with HIV will develop AIDS, said method comprising the
steps of: [0056] a) measuring the sIP-10 level in a sample of the
said subject; and [0057] b) determining the likelihood that said
subject will develop AIDS based on the level of step a).
[0058] As shown herein, a negative correlation has been
surprisingly found by the inventors between the levels of sIP-10
and the likelihood that a patient will progress towards AIDS. The
lower the sIP-10 levels, the higher the likelihood that the patient
will develop AIDS clinical symptoms.
[0059] In an embodiment of the present invention, the said method
comprises a prior step of obtaining a biological sample from the
said subject.
[0060] The present invention also provides a method for prognosing
an HIV disease in a subject identified as being infected with HIV,
said method comprising the steps of: [0061] a) measuring the sIP-10
level in a sample of the said subject; and [0062] b) prognosing the
said disease based on the level of step a).
[0063] In an embodiment of the present invention, the method for
prognosing an HIV disease in a subject infected with an HIV virus
includes a prior step of obtaining a biological sample from the
said subject.
[0064] As explained above, sIP-10 competes with IP-10 for CXCR3 and
has antagonistic properties. It is thus informative to express the
levels of sIP-10 as a ratio of sIP-10 versus total IP-10, instead
of as raw values of sIP-10 concentrations. As used herein, "total
IP-10" refers to all the IP-10 isoforms. In other words the total
IP-10 in a sample refers to all the IP-10(22-98) and sIP-10(24-98)
molecules present in the sample.
[0065] In fact, not only is SIP-10 a negative predictor of a rapid
progression of an HIV disease, the inventors have shown that the
ratio of sIP-10 to total IP-10 was decreased during acute HIV
infection in rapid progressors compared to the other HIV-infected
patients and compared to healthy subjects.
[0066] Therefore, in a preferred embodiment, the method of the
invention comprises a further step of measuring the total IP-10
level in the sample. According to another preferred embodiment, the
method of the invention comprises a further step of calculating the
ratio of sIP-10 to total IP-10. According to a further preferred
embodiment, the method of the invention comprises the steps of:
[0067] a) measuring the sIP-10 level in a biological sample of a
subject identified as being infected with HIV; [0068] b) measuring
the total IP-10 level in said sample of the said subject; [0069] c)
calculating the ratio of sIP-10 to total IP-10; and [0070] d)
prognosing the said disease based on the ratio of step c).
[0071] According to a further preferred embodiment, the method of
the invention comprises the steps of: [0072] a) obtaining a
biological sample from a subject identified as being infected with
HIV; [0073] b) measuring the sIP-10 level in said sample of the
said subject; [0074] c) measuring the total IP-10 level in said
sample of the said subject; [0075] d) calculating the ratio of
sIP-10 to total IP-10; and [0076] e) prognosing the said disease
based on the ratio of step d).
[0077] In an embodiment of the method of the invention, the level
of sIP-10 or the ratio of sIP-10 to total IP-10 is compared to a
reference value. The reference value corresponds for example to the
value of the said level or the said ratio in a healthy subject.
According to the present invention, a decreased level or ratio is
indicative of a bad prognosis, i.e. the subject presents a high
likelihood of progressing rapidly towards AIDS. In other words, the
said subject has a low likelihood of a long term survival. On the
other hand, an increased or a stable level or ratio is indicative
of a good prognosis. In this case, the subject displays a low
likelihood of progressing rapidly towards AIDS. In other words, the
said subject has a high likelihood of a long term survival.
HIV Infected Subjects
[0078] Following infection with HIV-1, the rate of clinical disease
progression varies between individuals. Factors such as host
susceptibility, genetics and immune function, health care and
co-infections as well as viral genetic variability[may affect the
rate of progression to the point of needing to take medication in
order not to develop AIDS. It is thus important to be capable of
identifying those who show a higher risk of progressing rapidly
towards AIDS.
[0079] HIV disease staging and classification systems are critical
tools providing clinicians and patients essential information for
clinical management. The CDC disease staging system assesses the
severity of the HIV disease by CD4.sup.+ T lymphocyte cell (CD4)
counts and by the presence of specific HIV-related conditions. This
system describes the infection in three stages: [0080] Stage 1: T
cell counts .gtoreq.500 cells/.mu.l and no AIDS defining
conditions; [0081] Stage 2: T cell counts 200 to 500 cells/.mu.l
and no AIDS defining conditions; and [0082] Stage 3: T cell counts
.ltoreq.200 cells/.mu.l or AIDS defining conditions.
[0083] Thus in an embodiment of the method of the invention, the
subject is selected in the group of subjects having T cell counts
of less than 200 cells/.mu.L, comprised between 200 and 500
cells/.mu.L, and above 500 cells/.mu.L. In another embodiment of
the method of the invention, the subject has T cell counts of less
than 200 cells/.mu.L. In another embodiment of the method of the
invention, the subject has T cell counts comprised between 200 and
500 cells/.mu.L. In another embodiment of the method of the
invention, the subject has T cell counts above 500 cells/.mu.L.
[0084] According to the CDC staging system, the definition of Al DS
includes all HIV-infected individuals with CD4 counts of less than
200 cells/.mu.L, or a CD4 percentage (over all lymphocytes) of less
than 14%, as well as those with certain HIV-related conditions and
symptoms. Furthermore, the CDC staging system classifies as
eligible for antiretroviral therapy subjects with CD4.sup.+
T-lymphocyte counts of less than 500 cells/.mu.L. Yet, some persons
having T cell counts above 500 cells/.mu.L are rapid progressors
who will advance towards AIDS in the next few months. Those people
may also benefit from antiretroviral therapy. It would thus be
beneficial to be capable of identifying those subjects which still
have T cell counts above 500 cells/.mu.L but have a high risk of
developing AIDS in the near future.
[0085] Thus in another embodiment, the method of the invention
relates to a method for determining the likelihood that a subject
identified as being infected with HIV and having T cell counts
above 500 cells/.mu.L will develop AIDS, said method comprising the
steps of: [0086] a) measuring the sIP-10 level in a sample of the
said subject; and [0087] b) determining the said likelihood based
on the level of step a).
[0088] In another aspect of the present invention, a method is
provided for determining the likelihood that a subject identified
as being infected with HIV and having T cell counts above 500
cells/.mu.L will develop AIDS. Generally, the method includes at
least the following steps: [0089] a) obtaining a biological sample
from a subject identified as being infected with HIV and having T
cell counts above 500 cells/.mu.L; [0090] b) measuring the sIP-10
level in said sample of the said subject; and [0091] c) determining
the said likelihood based on the level of step b).
[0092] In another embodiment, the method of the invention relates
to a method of prognosing an HIV disease in a subject identified as
being infected with HIV and having T cell counts above 500
cells/.mu.L, said method comprising the steps of: [0093] a)
measuring the sIP-10 level in a sample of the said subject; and
[0094] b) prognosing the said disease based on the level of step
a).
[0095] In another aspect of the present invention, a method is
provided for prognosing an HIV disease in a subject infected with
an HIV virus and having T cell counts above 500 cells/.mu.L.
Generally, the method includes at least the following steps: [0096]
a) obtaining a biological sample from a subject identified as being
infected with HIV and having T cell counts above 500 cells/.mu.L;
[0097] b) measuring the sIP-10 level in said sample of the said
subject; and [0098] c) prognosing the said disease based on the
level of step b).
[0099] In a preferred embodiment, the method of the invention
comprises a further step of measuring the total IP-10 level in the
sample. According to another preferred embodiment, the method of
the invention comprises a further step of calculating the ratio of
sIP-10 to total IP-10. According to a further preferred embodiment,
the method of the invention comprises the steps of: [0100] a)
measuring the sIP-10 level in a biological sample from a subject
identified as being infected with HIV and having T cell counts
above 500 cells/.mu.L; [0101] b) measuring the total IP-10 level in
said sample of the said subject; [0102] c) calculating the ratio of
sIP-10 to total IP-10; and [0103] d) prognosing the said disease
based on the ratio of step c).
[0104] According to a further preferred embodiment, the method of
the invention comprises the steps of: [0105] a) obtaining a
biological sample from a subject identified as being infected with
HIV and having T cell counts above 500 cells/.mu.L; [0106] b)
measuring the sIP-10 level in said sample of the said subject;
[0107] c) measuring the total IP-10 level in said sample of the
said subject; [0108] d) calculating the ratio of sIP-10 to total
IP-10; and [0109] e) prognosing the said disease based on the ratio
of step d).
[0110] In an embodiment of the method of the invention, the level
of sIP-10 or the ratio of sIP-10 to total IP-10 is compared to a
reference value. The reference value corresponds for example to the
value of the said level or the said ratio in a healthy subject.
According to the present invention, a decreased level or ratio is
indicative of a bad prognosis, i.e. the subject presents a high
likelihood of progressing rapidly towards AIDS. In other words, the
said subject has a low likelihood of a long term survival. On the
other hand, an increased or a stable level or ratio is indicative
of a good prognosis. In this case, the subject displays a low
likelihood of progressing rapidly towards AIDS. In other words, the
said subject has a high likelihood of a long term survival.
[0111] Human dipeptidyl peptidase IV (DPPIV), which is also known
as CD26, is a 110 kDa cell surface molecule. The amino acid
sequence of human DPPIV protein comprises 766 amino acids and is
shown in SEQ ID NO: 3 (Swissprot database Accession No. P27487). It
contains intrinsic dipeptidyl peptidase IV activity which
selectively removes N-terminal dipeptide from peptides with proline
or alanine in the third amino acid position. It interacts with
various extracellular molecules and is also involved in
intracellular signal transduction cascades. The multifunctional
activities of human DPPIV are dependent on cell type and
intracellular or extracellular conditions that influence its role
as a proteolytic enzyme, cell surface receptor, co-stimulatory
interacting protein and signal transduction mediator. Human DPPIV
has a short cytoplasmatic domain from amino acid position 1 to 6, a
transmembrane region from amino acid position 7 to 28, and an
extracellular domain from amino acid position 29 to 766 with
intrinsic dipeptidyl peptidase IV (DPPIV) activity.
[0112] It has been shown in the literature that IP-10 is cleaved by
DPPIV, resulting in the generation of a short form of IP-10
(sIP-10) that acts as an antagonist of CXCR3 (De Meester et al,
1999, Immunol Today, 20(8): 367-375).
[0113] The inventors have shown that plasma DPPIV activity is
reduced during acute infection in those HIV-infected patients who
subsequently progressed more rapidly than the other patients
towards AIDS, just like the level of sIP-10. In other words, the
activity of DPPIV can be used as a convenient proxy for the level
of SIP-10.
[0114] The present invention thus also relates to a method of
determining the likelihood that a subject identified as being
infected with HIV will develop AIDS, said method comprising the
steps of: [0115] a) measuring the DPPIV activity in a sample of the
said subject; and [0116] b) determining the likelihood that said
subject will develop AIDS based on the level of step a).
[0117] In an embodiment of the present invention, the said method
comprises a prior step of obtaining a biological sample from the
said subject.
[0118] The present invention also provides a method for prognosing
an HIV disease in a subject identified as being infected with HIV,
said method comprising the steps of: [0119] a) measuring the DPPIV
activity in a sample of the said subject; and [0120] b) prognosing
the said disease based on the level of step a).
[0121] In an embodiment of the present invention, the method for
prognosing an HIV disease in a subject infected with an HIV virus
includes a prior step of obtaining a biological sample from the
said subject.
[0122] In an embodiment of the method of the invention, the DPPIV
activity is compared to a reference value. The reference value
corresponds for example to the value of the said activity in a
healthy subject. According to the present invention, a decreased
activity is indicative of a bad prognosis, i.e. the subject
presents a high likelihood of progressing rapidly towards AIDS. In
other words, the said subject has a low likelihood of a long term
survival. On the other hand, an increased or a stable activity is
indicative of a good prognosis. In this case, the subject displays
a low likelihood of progressing rapidly towards AIDS. In other
words, the said subject has a high likelihood of a long term
survival.
[0123] In another aspect, the method of the invention relates to a
method of prognosing an HIV disease in a subject identified as
being infected with HIV and having T cell counts above 500
cells/.mu.L, said method comprising the steps of: [0124] a)
measuring the DPPIV activity in a sample of the said subject; and
[0125] b) prognosing the said disease based on the activity of step
a).
[0126] In an embodiment of the present invention, the said method
comprises a prior step of obtaining a biological sample from the
said subject.
[0127] In an embodiment of the method of the invention, the
activity of DPPIV is compared to a reference value. The reference
value corresponds for example to the value of the said activity in
a healthy subject. According to the present invention, a decreased
activity is indicative of a bad prognosis, i.e. the subject
presents a high likelihood of progressing rapidly towards AIDS. In
other words, the said subject has a low likelihood of a long term
survival. On the other hand, an increased or a stable activity is
indicative of a good prognosis. In this case, the subject displays
a low likelihood of progressing rapidly towards AIDS. In other
words, the said subject has a high likelihood of a long term
survival.
[0128] For the methods herein, the biological sample is preferably
a sample from blood, plasma, lymph, bone marrow fluid, pleural
fluid, peritoneal fluid, spinal fluid, abdominal fluid, pancreatic
fluid, cerebrospinal fluid, brain fluid, ascites, urine, saliva,
bronchial lavage, bile, sweat, tears, ear flow, sputum, semen,
vaginal flow, milk, amniotic fluid, or secretions of respiratory,
intestinal or genitourinary tract. Exemplary of such samples, is a
peripheral blood sample, and a body fluid sample that contains
dissociated bone marrow cells from a bone marrow biopsy. The volume
of sample is any that is convenient for testing, such as at least
about 0.01 mL to about 50 mL or 100 ml.
[0129] The preparation and/or isolation of proteinaceous material
from a sample for analysis are also well known in this field.
Antibodies for sIP-10 and IP-10
[0130] Measuring the levels of sIP-10 expression in a sample is
easily undertaken by one knowledgeable in this field. Non-limiting
examples include western-blot analysis, ELISA assays,
immuno-reactivity assays, column assays using fluorescence,
antibodies and radiolabeled markers. Automated manners of
performing the analysis, for example, using a computer processor
can also be used.
[0131] Total, long and short (truncated) IP-10 can be determined
utilizing polyclonal (rabbit) and monoclonal (mouse) antibodies
that are specific for the long form of IP-10. In an added
embodiment, in vivo IP-10 activity can be assessed by using CXCR3
cells as a surrogate for IP-10 activity. Flow cytometry can be used
to measure the relative amount of CXCR3 cells in the peripheral
blood of patients throughout their treatment. This will serve as a
reflection of the ability of activated T cells and B cells to
respond to a gradient of IP-10 (keeping in mind that there exist
other CXCR3 agonists). In another added embodiment, a dipeptidyl
peptidase IV activity can be measured in patient plasma, which can
correlate to the IP-10 cleavage.
[0132] In this analysis, it is advantageous to inactivate the
plasma DPPIV activity, thus preventing an extra-corporeal cleavage
of IP-10. Collections are thus preferably performed with protease
inhibitors. For example, one such commercially available sample
collection tube is BD.TM. P700 but other such BD.TM. 100 are also
sufficient to preserve IP-10 in its circulating form.
[0133] In one embodiment, antibodies specific for the long form of
IP-10 to evaluate the amount of long vs. short form of IP-10 are
generated. Such antibodies that distinguish full-length IP-10 from
short (truncated) form of IP-10, were generated by immunization of
rabbits with a synthetic peptide coupled to KLH; (VPLSRTVRC
(positions 22-30 of NP.sub.--001556; SEQ ID NO: 4) corresponding of
the NH.sub.2 terminal of the full-length IP-10 protein).
Immunoglobulins G (IgG) can then be purified in two steps by
chromatography affinity: the first step is a positive selection of
IgG that recognize the long peptide. The second step is depletion
of IgG that recognize the shorter peptide LSRTVRC (SEQ ID NO: 4)
common to short and full-length form of IP-10. Purified antibodies
are specific to full-length IP-10. The same strategy can be used to
obtain polyclonal antibodies from different species (e.g., goat,
chicken, and others). Monoclonal antibodies may also be derived
from mice after immunization with the long peptide. After verifying
the presence of antibody production in the serum, hybridomas are
produced and cloned. The hybridoma screening can be made by direct
ELISA with both, the long and short peptides, and the full-length
and short form of recombinant IP-10 coated directly in ELISA plate.
Then antibodies from hybridomas specific of the full-length can be
purified. Validation of polyclonal antibodies can be performed by
direct and by sandwiches Elisa assays against short and full-length
IP-10 form. SIP-10 can be generated by following in vitro digestion
of recombinant full-length IP-10 by recombinant DPIV. The two
NH.sub.2 amino-acids, Valine and Proline are truncated from the
full-length. Monoclonal antibodies discriminating between the short
and the long forms of IP-10 have been described in e.g. U.S. Pat.
No. 8,124,332 and in Casrouge et al., J Clin Invest., 121(1):
308-317, 2011.
sIP-10 Levels Assay
[0134] Using these distinguishing antibodies, IP-10 can be detected
in biological fluids, for example, using an ELISA assay to
specifically detect the full-length IP-10. As IP-10 binds to
heparin, heparin cross-linked to agarose beads via amide bonds can
be used to concentrate IP-10 from plasma. IP-10 can be eluted with
NaCl 1M. To avoid or at least minimize ex vivo truncation of IP-10
in biologic samples, inhibitors of DPIV can be added into
collection tubes. Various DPIV inhibitors are known in the art,
e.g., a large number of DPIV inhibitors have been described and
their structures and characteristics have been succinctly reviewed
(see e.g. U.S. Pat. No. 4,935,493; U.S. Pat. No. 5,462,928; U.S.
Pat. No. 5,543,396; U.S. Pat. No. 5,296,604; U.S. Pat. No.
6,100,234; PCT/US92/09845; Augustyns et al., Curr Med Chem., 6(4):
311-327, 1999; Evans, IDrugs, 5: 577-585, 2002; Weber, J Med Chem.,
47(17): 4135-4141, 2004; McIntosh et al., Int J Biochem & Cell
Biol, 38(5-6): 860-872, 2006; Wiedeman & Trevillyan, Curr Opin
Investig Drugs, 4(4): 412-420; 2003). The HuCAl (Human
Combinatorial Antibody library) technology allows to generate in
vitro a 1.5 billion human antibodies candidates library. An
automated panning process is used: the peptides specific of long
and short forms of IP-10 are immobilized in 384-well microplate for
screening against antibody-displaying phage library. Specificity of
antibodies is then verified by ELISA.
[0135] To generate the short (truncated) IP-10 form, the full
length IP-10 sequence
(VPLSRTVRCTCISISNQPVNPRSLEKLEIIPASQFCPRVEIIATMKKKGEKRCLNPESKAIKN-
LLKAVSKE MSKRSP, SEQ ID NO: 1) can be incubated with DPIV at
25-37.degree. C. to generate the short form
(LSRTVRCTCISISNQPVNPRSLEKLEIIPASQFCPRVEIIATMKKKGEKRCLNPESKAIKNLLKAVSKEM
SKRSP, SEQ ID NO: 2). DPIV is a known protein, with a cloned
sequence (e.g., from mammals such as human and mouse). Resolution
of IP-10 and sIP-10 can be accomplished by Western blotting or by
MALDI-TOF-MS as is known in the art.
[0136] In other embodiments, the antibodies that distinguish
between the short and long forms of IP-10 can be used to evaluate
patients with chronic inflammation (e.g., cancer, obesity,
autoimmunity, graft vs. host disease). Specific applications can be
focused on diseases in which IP-10 and/or DPIV have been shown to
be elevated (e.g., melanoma, type II diabetes, autoimmune
vasculitis).
Soluble DPPIV Expression
[0137] Human soluble dipeptidyl peptidase IV (soluble DPPIV) amino
acid sequence is shown in SEQ ID NO: 3, and comprises the amino
acid positions 29 to 766 from Swissprot database Accession number
P27487. The dimer of soluble DPPIV is a 170 kDa glycoprotein
consisting of two identical monomeric soluble DPPIV units.
[0138] To express a soluble DPPIV enzyme, the polynucleotide can be
inserted into an expression vector which contains the necessary
elements for the transcription and translation of the inserted
coding sequence. Methods which are well known to those skilled in
the art can be used to construct expression vectors containing
sequences encoding a soluble DPPIV polypeptide and appropriate
transcriptional and translational control elements. These methods
include in vitro recombinant DNA techniques, synthetic techniques,
and in vivo genetic recombination. Such techniques are described,
for example, in Sambrook et al. (1989) and in Ausubel et al
(1989).
[0139] A variety of expression vector/host systems can be utilized
to contain and express sequences encoding a soluble DPPIV
polypeptide. These include, but are not limited to, microorganisms,
such as bacteria transformed with recombinant bacteriophage,
plasmid, or cosmid DNA expression vectors; yeast transformed with
yeast expression vectors, insect cell systems infected with virus
"expression vectors (e.g., baculovirus), plant cell systems
transformed with virus expression vectors (e.g., cauliflower mosaic
virus, CaMV; tobacco mosaic virus, TMV) or with bacterial
expression vectors (e.g., Ti or pBR322 plasmids), or animal cell
systems.
[0140] The control elements or regulatory sequences are those
nontranslated regions of the vector enhancers, promoters, 5' and 3'
untranslated regions which interact with host cellular proteins to
carry out transcription and translation. Such elements can vary in
their strength and specificity. Depending on the vector system and
host utilized, any number of suitable transcription and translation
elements, including constitutive and inducible promoters, can be
used. For example, when cloning in bacterial systems, inducible
promoters such as the hybrid lacZ promoter of the BLUESCRIPT
phagemid (Stratagene, LaJolla, Calif.) or pSPORTI plasmid (Life
Technologies) and the like can be used. The baculovirus polyhedrin
promoter can be used in insect cells. Promoters or enhancers
derived from the genomes of plant cells (e.g., heat shock, RUBISCO,
and storage protein genes) or from plant viruses (e.g., viral
promoters or leader sequences) can be cloned into the vector. In
mammalian cell systems, promoters from mammalian genes or from
mammalian viruses are preferable. If it is necessary to generate a
cell line that contains multiple copies of a nucleotide sequence
encoding a soluble DPPIV enzyme polypeptide, vectors based on SV40
or EBV can be used with an appropriate selectable marker.
DPPIV Assay
[0141] Assays for DPPIV activity are well known in the art. DPPIV
activity can be assayed using a substrate which reacts with DPPIV
to form a detectable product, as described in U.S. Pat. No.
5,601,986. Suitable enzyme substrates include, but are not limited
to, dipeptide substrates such as Xaa-pro-para-nitro-analide
(Xaa-Pro-PNA) or Xaa-Pro-coumarin. The variable amino acid, Xaa,
can be any naturally occurring or synthetic amino acid. An
exemplary dipeptide substrate is Gly-Pro-para-nitro-analide
(Gly-Pro-PNA). At a wavelength of 405 nanometers, the substrate has
no absorbance; however, if the dipeptide substrate is cleaved
(after the Pro) due to the presence of DPPIV, the formation of a
reaction product can be visualized spectrophotometrically, as a
yellow-green color is produced. Other substrates, such as
Xaa-Pro-coumarin, can be visualized spectrofluorometrically as a
fluorescent emission is produced by the reaction.
[0142] DPPIV assays embodying such reagents and reactions can be
performed in any suitable reaction vessel, for example, a test tube
or well of a microtiter plate. Enzyme activities typically are
measured at 24.degree. C., by mixing 50 or 100 .mu.l of enzyme
sample to 100 or 150 .mu.l microliters of a reaction buffer
containing 200 .mu.M of chromogenic substrate, such as Gly-Pro-PNA
(commercially available from Bachem, San Diego, Calif.) in 0.1 M
Tris-HCl buffered Triton X-100 (0.1% v/v) at pH 7.0. The reactions
are incubated for 30 minutes, and optical density readings are
taken at 405 nm. During the reaction time course, several optical
density readings are taken at different time points. DPPIV enzyme
activity is expressed in nmol/min/ml based on the progression curve
calculated from the concentration of hydrolyzed substrates.
Methods of Treatment
[0143] A subject identified as being infected with HIV and who has
a bad prognosis would benefit from being treated with an anti-HIV
therapy before the appearance of the AIDS symptoms.
[0144] A practitioner treats HIV infection by taking actions to
ameliorate the causes or symptoms of the infection in a patient.
Treatment of HIV comprises administering therapy to a patient.
Therapy may include: selecting and administering one or more
anti-HIV drugs to the patient, adjusting the dosage of the anti-HIV
drug, adjusting the dosing schedule of the drug, and adjusting the
length of the therapy. Anti-HIV drugs are selected by practitioners
based on the nature of the infection, the patient's response to the
infection and the patient's response to the drug. The dosage of the
anti-HIV drug can be adjusted as well by the practitioner based on
the nature of the drug, the nature of the infection, the patient's
response to the infection, and the patient's response to the drug.
The dosing schedule can also be adjusted by the practitioner based
on the nature of the drug, the nature of the infection, the
patient's response to the infection, and the patient's response to
the drug. Also, the length of the therapy can be adjusted by the
practitioner based on the nature of the drug, the nature of the
infection, the patient's response to the infection, the patient's
response to the drug. Also, the practitioner can select between a
single drug therapy, a dual drug therapy, or a triple drug therapy.
Also, the anti-HIV therapy can be adjusted by the practitioner
based on whether the patient suffers from acute HIV infection,
chronic HIV infection or AIDS.
[0145] Antiretroviral or anti-HIV disease therapy can include, but
is not limited to, highly active antiretroviral therapy (HAART),
protease inhibitors, fusion inhibitors, integrase inhibitors,
co-receptor specific agents, 3TC, AZT, nevirapine, non-nucleoside
analogue reverse transcriptase inhibitors and nucleoside analogue
reverse transcriptase inhibitors. HAART can be three or more
antiretroviral drugs in combination, including at least one
protease inhibitor, or at least a reverse transcriptase inhibitor
and a protease inhibitor; or at least two reverse transcriptase
inhibitors with at least one protease inhibitor.
[0146] Typical reverse transcriptase inhibitors include nucleoside
analogs, e.g., AZT (Zidovudine), ddi (didanosine), ddc
(zalcitabine), D4T (stavudine), 3TC (lamivudine), Ziagen
(abacavir), combivir (mix of AZT and 3TC), and non-nucleoside
analogs, e.g., viramune (nevirapine), rescriptor (delavirdine),
sustiva (efavirenz). Protease inhibitors include invirase
(saquinavir), norvir (ritonavir), crixivan (indinavir), viracept
(nelfinavir), agenerase (amprenivir), kaletra (lopinavir and
ritonavir) and fortovase (saquinavir in a soft gelatin form). Thus,
HAART can also be "triple cocktail" therapy. That is, a three drug
regimen is used to combat HIV wherein one of the three drugs is
usually a protease inhibitor (and the other two are usually reverse
transcriptase inhibitors).
[0147] In a particular aspect, the invention relates to a method
for selecting an anti-HIV therapy for a subject identified as being
infected with HIV. Generally, the method of the invention comprises
at least the following steps: [0148] a) determining the likelihood
that said subject will develop AIDS by any one of the above
methods; and [0149] b) selecting the therapy based on the said
likelihood.
[0150] In one embodiment the invention relates to a method for
selecting an anti-HIV therapy for a subject identified as being
infected with HIV. Generally, the method of the invention comprises
at least the following steps: [0151] a) determining the prognosis
of the said subject by any one of the above methods; and [0152] b)
selecting the therapy based on the said prognosis.
[0153] In one embodiment the therapy is selected from the group
consisting of: highly active antiretroviral therapy (HAART),
protease inhibitors, fusion inhibitors, integrase inhibitors,
co-receptor specific agents, 3TC, AZT, nevirapine, non-nucleoside
analogue reverse transcriptase inhibitors, nucleoside analogue
reverse transcriptase inhibitors and vaccine therapy.
[0154] HIV-infected subjects who efficiently control viral
replication because they are under anti-HIV therapy, e.g. HAART
regimen, still display low levels of chronic inflammation.
HIV-infected subjects, who interrupt antiretroviral treatment,
generally display a strong viral rebound. During this viral
rebound, the subjects are highly transmissible for HIV.
Interestingly, between 5 and 15% of HIV-infected subjects who
started HIV therapy, e.g., HAART, early, spontaneously control
viral replication after treatment interruption. More generally, it
would be advantageous to be capable of monitoring the efficacy of
anti-HIV therapy for subjects identified as being infected with
HIV. In particular, it would thus be useful to be capable of
identifying the subjects who have a high likelihood of controlling
viral replication and not developing AIDS. These subjects would
thus benefit from arresting their treatment. Alternatively, it
would be useful to identify the subjects who have a high likelihood
of progressing towards AIDS if their treatment was stopped. These
patients should be maintained on an HIV therapy.
[0155] The present invention thus provides a method for monitoring
the efficacy of an anti-HIV therapy for a subject identified as
being infected with HIV, said method comprising the steps of:
[0156] a) determining the likelihood that said subject will develop
AIDS by any one of the above methods; and [0157] b) assessing the
efficacy of said therapy based on the determination of step a).
[0158] Efficacy of HIV treatment can be determined using the
methods provided herein. In particular examples, the level of
sIP-10 or the ratio of sIP-10 to total IP-10 or the activity of
DPPIV is measured at a first time point using the methods provided
and then compared to the level of sIP-10 or the ratio of sIP-10 to
total IP-10 or the activity of DPPIV, respectively, measured at a
second later time point by the same method. In some examples, the
first time point is at a predetermined time prior to administration
of a therapy, such as an anti-HIV therapy, and the second time
point is at a predetermined time following administration of the
therapy, during the administration of the therapy, or between
successive administrations of the therapy. In exemplary methods,
the sample can be obtained from the subject, for example, at least,
at about or at 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours,
7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours,
14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20
hours, 21 hours, 22 hours, 23 hours, 1 day, 2 days, 3 days, 4 days,
5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days,
13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20
days, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9
weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks,
16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, or later
following administration of the anti-HIV therapy to the subject. In
some examples, samples are collected at a plurality of time points,
such as at more than one time point, including, for example, at 1,
2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more time points following
administration of the anti-HIV therapy to the subject. In some
examples, samples are collected at regular intervals following
administration of the anti-HIV therapy to the subject.
[0159] In particular examples, the level of sIP-10 or the ratio of
sIP-10 to total IP-10 or the activity of DPPIV is measured at a
first time and then compared to the level of sIP-10 or the ratio of
sIP-10 to total IP-10 or the activity of DPPIV, respectively,
measured at a second later time point to determine the likelihood
of developing AIDS over time, where if the level of sIP-10 or the
ratio of sIP-10 to total IP-10 or the activity of DPPIV at the
second time point is more than the level of sIP-10 or the ratio of
sIP-10 to total IP-10 or the activity of DPPIV, respectively, at
the first time point, then the likelihood that the subject will
develop AIDS has decreased. In particular examples, if the level of
sIP-10 or the ratio of sIP-10 to total IP-10 or the activity of
DPPIV at a second time point is 2, 3, 4, 5, 6, 7, 8, 8, 9, 10, 20,
30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800,
900, 1000 or more times greater than the level of sIP-10 or the
ratio of sIP-10 to total IP-10 or the activity of DPPIV,
respectively, at a first time point, then the likelihood that the
subject will develop AIDS has decreased.
[0160] In particular examples, the level of sIP-10 or the ratio of
sIP-10 to total IP-10 or the activity of DPPIV is measured at a
first time and then compared to the level of sIP-10 or the ratio of
sIP-10 to total IP-10 or the activity of DPPIV, respectively,
measured at a second later time point to determine stabilization of
the likelihood to progress towards AIDS over time, where if the
level of sIP-10 or the ratio of sIP-10 to total IP-10 or the
activity of DPPIV at the second time point is equal to or about the
same as the level of sIP-10 or the ratio of sIP-10 to total IP-10
or the activity of DPPIV at the first time point, then the
likelihood to progress towards AIDS has stabilized.
[0161] In particular examples, the level of sIP-10 or the ratio of
sIP-10 to total IP-10 or the activity of DPPIV is measured at a
first time point and then compared to the level of sIP-10 or the
ratio of sIP-10 to total IP-10 or the activity of DPPIV,
respectively, measured at a second later time point to determine
the effectiveness of therapy in inhibiting HIV disease progression,
where if the level of sIP-10 or the ratio of sIP-10 to total IP-10
or the activity of DPPIV at the second time point is more than or
equal to the level of sIP-10 or the ratio of sIP-10 to total IP-10
or the activity of DPPIV, respectively, at the first time point,
then the therapy is effective at inhibiting HIV disease
progression. In particular examples, if the level of sIP-10 or the
ratio of sIP-10 to total IP-10 or the activity of DPPIV at a second
time point is equal to or 2, 3, 4, 5, 6, 7, 8, 8, 9, 10, 20, 30,
40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800,
900, 1000 or more times greater than the level of sIP-10 or the
ratio of sIP-10 to total IP-10 or the activity of DPPIV,
respectively, at a first time point, then the therapy is effective
at inhibiting HIV disease progression.
[0162] In particular examples, the level of sIP-10 or the ratio of
sIP-10 to total IP-10 or the activity of DPPIV is measured at a
first time point and then compared to the level of sIP-10 or the
ratio of sIP-10 to total IP-10 or the activity of DPPIV,
respectively, measured at a second later time point to determine
the effectiveness of therapy in inhibiting HIV disease progression,
where if the level of sIP-10 or the ratio of sIP-10 to total IP-10
or the activity of DPPIV at the first time point is greater than
the level of sIP-10 or the ratio of sIP-10 to total IP-10 or the
activity of DPPIV, respectively, at the second time point, then the
therapy is not effective at inhibiting HIV disease progression. In
particular examples, if the level of sIP-10 or the ratio of sIP-10
to total IP-10 or the activity of DPPIV at a first time point is 2,
3, 4, 5, 6, 7, 8, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100,
200, 300, 400, 500, 600, 700, 800, 900, 1000 or more times greater
than the level of sIP-10 or the ratio of sIP-10 to total IP-10 or
the activity of DPPIV, respectively, at a second time point, then
the therapy is not effective at inhibiting HIV disease
progression.
[0163] In some examples, the methods provided herein can detect at
or about a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold,
9-fold, 10-fold, 200-fold, 300-fold, 400-fold, 500-fold, 600-fold,
700-fold, 800-fold, 900-fold, 1000-fold or higher increase in the
level of sIP-10 or the ratio of sIP-10 to total IP-10 or the
activity of DPPIV over time relative to a control sample. in
particular examples, the methods provided herein can detect at or
about a 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold,
9-fold, 10-fold, 200-fold, 300-fold, 400-fold, 500-fold, 600-fold,
700-fold, 800-fold, 900-fold, 1000-fold or higher decrease in the
level of sIP-10 or the ratio of sIP-10 to total IP-10 or the
activity of DPPIV over time relative to a control sample. In some
examples, the control sample is a sample obtained from a subject at
a first time point and compared to a sample obtained from the
subject at a second time point. In some examples, the control
sample is a sample with a known level of sIP-10 or ratio of sIP-10
to total IP-10 or activity of DPPIV. In some examples, the control
sample is a sample obtained from a subject with a particular HIV
disease, a known stage of HIV disease, or a known HIV disease
prognosis.
[0164] The present invention further relates to a method for
adjusting a HIV therapy for a subject identified as being infected
with HIV, said method comprising the steps of: [0165] a) assessing
the efficacy of an anti-HIV therapy for said subject by any one of
the above methods; and [0166] b) adapting the said treatment based
on said assessment.
[0167] Said adaptation of the HIV therapy may consist in: [0168] a
reduction or suppression of the said HIV therapy if the therapy is
assessed as being effective, or [0169] the continuation or an
augmentation of the said HIV therapy if the therapy is assessed as
not being effective.
[0170] In one embodiment, the practitioner adjusts the therapy
based on the patient's level of sIP-10 or ratio of sIP-10 to total
IP-10 or activity of DPPIV compared to a reference level. In one
embodiment, the practitioner adjusts the therapy by selecting and
administering a different drug. In one embodiment, the practitioner
adjusts the therapy by selecting and administering a different
combination of drugs. In one embodiment, the practitioner adjusts
the therapy by adjusting drug dosage. In one embodiment, the
practitioner adjusts the therapy by adjusting dose schedule. In one
embodiment, the practitioner adjusts the therapy by adjusting
length of therapy. In one embodiment, the practitioner adjusts the
therapy by selecting and administering a different drug combination
and adjusting drug dosage. In one embodiment, the practitioner
adjusts the therapy by selecting and administering a different drug
combination and adjusting dose schedule. In one embodiment, the
practitioner adjusts the therapy by selecting and administering a
different drug combination and adjusting length of therapy. In one
embodiment, the practitioner adjusts the therapy by adjusting drug
dosage and dose schedule. In one embodiment, the practitioner
adjusts the therapy by adjusting drug dosage and adjusting length
of therapy. In one embodiment, the practitioner adjusts the therapy
by adjusting dose schedule and adjusting length of therapy. In one
embodiment, the practitioner adjusts the therapy by selecting and
administering a different drug, adjusting drug dosage, and
adjusting dose schedule. In one embodiment, the practitioner
adjusts the therapy by selecting and administering a different
drug, adjusting drug dosage, and adjusting length of therapy. In
one embodiment, the practitioner adjusts the therapy by selecting
and administering a different drug, adjusting dose schedule, and
adjusting length of therapy. In one embodiment, the practitioner
adjusts the therapy by adjusting drug dosage, adjusting dose
schedule, and adjusting length of therapy. In one embodiment, the
practitioner adjusts the therapy by selecting and administering a
different drug, adjusting drug dosage, adjusting dose schedule, and
adjusting length of therapy.
[0171] In one embodiment, therapy comprises the selection and
administration of an anti-HIV drug to the patient by the
practitioner. In one embodiment, the anti-HIV disease drug
comprises protease inhibitors. In one embodiment, the anti-HIV
disease drug comprises fusion inhibitors. In one embodiment, the
anti-HIV disease drug comprises integrase inhibitors. In one
embodiment, the anti-HIV disease drug comprises co-receptor
specific agents. In one embodiment, the anti-HIV disease drug
comprises 3TC. In one embodiment, the anti-HIV disease drug
antiviral interferon comprises AZT. In one embodiment, the anti-HIV
disease drug comprises polymerase inhibitor. In one embodiment, the
anti-HIV disease drug comprises protease inhibitor. In one
embodiment, the anti-HCV drug comprises nevirapine. In one
embodiment, the anti-HIV disease drug comprises non-nucleoside
analogue reverse transcriptase inhibitors. In one embodiment, the
anti-HIV disease drug comprises nucleoside analogue reverse
transcriptase inhibitors.
[0172] In another embodiment, therapy comprises the selection and
administration of two anti-HIV disease drugs to the patient by the
practitioner as part of dual therapy. In one embodiment the two
dual therapy drugs are protease inhibitors. In one embodiment the
two dual therapy drugs are non-nucleoside analogue reverse
transcriptase inhibitors. In one embodiment the two dual therapy
drugs are nucleoside analogue reverse transcriptase inhibitors. In
one embodiment the two dual therapy drugs are a protease inhibitor
and a non-nucleoside analogue reverse transcriptase inhibitor. In
one embodiment the two dual therapy drugs are a protease inhibitor
and a nucleoside analogue reverse transcriptase inhibitor. In one
embodiment the two dual therapy drugs are a non-nucleoside analogue
reverse transcriptase inhibitor and nucleoside analogue reverse
transcriptase inhibitor.
[0173] In another embodiment, therapy comprises the selection and
administration of three anti-HIV disease drugs to the patient by
the practitioner as part of triple therapy. In one embodiment the
three triple therapy drugs are an interferon drug, ribavirin, and a
NS3 protease inhibitor. In one embodiment, the triple therapy drugs
comprise highly active antiretroviral therapy (HAART). In one
embodiment, the anti-HIV disease drug comprises HAART, said HAART
being three or more antiretroviral drugs in combination, including
at least one protease inhibitor. In one embodiment, the anti-HIV
disease drug comprises HAART, said HAART being three or more
antiretroviral drugs in combination, including at least a reverse
transcriptase inhibitor and a protease inhibitor. In one
embodiment, the anti-HIV disease drug comprises HAART, said HAART
being three or more antiretroviral drugs in combination, including
at least two reverse transcriptase inhibitors with at least one
protease inhibitor.
[0174] In one embodiment where there is an decreased level of level
of sIP-10 or ratio of sIP-10 to total IP-10 or activity of DPPIV
with respect to a reference level, treatment comprises a less
aggressive therapy than a reference therapy. In one embodiment a
less aggressive therapy comprises not administering drugs and
taking a "watchful waiting" approach. In one embodiment a less
aggressive therapy comprises delaying administration of anti-HIV
disease drugs. In one embodiment a less aggressive therapy
comprises selecting and administering less potent drugs. In one
embodiment a less aggressive therapy comprises decreasing dosage of
anti-HIV disease drugs. In one embodiment a less aggressive therapy
comprises decreasing the frequency of the dose schedule. In one
embodiment a less aggressive therapy comprises shortening length of
therapy. In one embodiment, less aggressive therapy comprises
selecting and administering less potent drugs and decreasing drug
dosage. In one embodiment, less aggressive therapy comprises
selecting and administering less potent drugs and decreasing dose
schedule. In one embodiment, less aggressive therapy comprises
selecting and administering less potent drugs and shortening length
of therapy. In one embodiment, less aggressive therapy comprises
decreasing drug dosage and decreasing dose schedule. In one
embodiment, less aggressive therapy comprises decreasing drug
dosage and shortening length of therapy. In one embodiment, less
aggressive therapy comprises decreasing dose schedule and
shortening length of therapy. In one embodiment, less aggressive
therapy comprises selecting and administering less potent drugs,
decreasing drug dosage, and decreasing dose schedule. In one
embodiment, less aggressive therapy comprises selecting and
administering less potent drugs, decreasing drug dosage, and
shortening length of therapy. In one embodiment, less aggressive
therapy comprises selecting and administering less potent drugs,
decreasing dose schedule, and shortening length of therapy. In one
embodiment, less aggressive therapy comprises decreasing drug
dosage, decreasing dose schedule, and shortening length of therapy.
In one embodiment, less aggressive therapy comprises selecting and
administering less potent drugs, decreasing drug dosage, decreasing
dose schedule, and shortening length of therapy.
[0175] In one embodiment a less aggressive therapy comprises
selecting and administering a single therapy instead of a dual
therapy. In one embodiment a less aggressive therapy comprises
delaying administration of anti-HIV disease drugs and selecting and
administering a single therapy instead of a dual therapy. In one
embodiment a less aggressive therapy comprises selecting and
administering a single therapy instead of a dual therapy and
selecting and administering less potent drugs. In one embodiment a
less aggressive therapy comprises selecting and administering a
single therapy instead of a dual therapy and decreasing dosage of
anti-HIV disease drugs. In one embodiment a less aggressive therapy
comprises selecting and administering a single therapy instead of a
dual therapy and decreasing the frequency of the dose schedule. In
one embodiment a less aggressive therapy comprises selecting and
administering a single therapy instead of a dual therapy and
shortening length of therapy. In one embodiment, less aggressive
therapy comprises selecting and administering a single therapy
instead of a dual therapy and selecting and administering less
potent drugs and decreasing drug dosage. In one embodiment, less
aggressive therapy comprises selecting and administering a single
therapy instead of a dual therapy and selecting and administering
less potent drugs and decreasing dose schedule. In one embodiment,
less aggressive therapy comprises selecting and administering a
single therapy instead of a dual therapy, selecting and
administering less potent drugs and shortening length of therapy.
In one embodiment, less aggressive therapy comprises selecting and
administering a single therapy instead of a dual therapy,
decreasing drug dosage and decreasing dose schedule. In one
embodiment, less aggressive therapy comprises selecting and
administering a single therapy instead of a dual therapy,
decreasing drug dosage and shortening length of therapy. In one
embodiment, less aggressive therapy comprises selecting and
administering a single therapy instead of a dual therapy,
decreasing dose schedule and shortening length of therapy. In one
embodiment, less aggressive therapy comprises selecting and
administering a single therapy instead of a dual therapy, selecting
and administering less potent drugs, decreasing drug dosage, and
decreasing dose schedule. In one embodiment, less aggressive
therapy comprises selecting and administering a single therapy
instead of a dual therapy, selecting and administering less potent
drugs, decreasing drug dosage, and shortening length of therapy. In
one embodiment, less aggressive therapy comprises selecting and
administering a single therapy instead of a dual therapy, selecting
and administering less potent drugs, decreasing dose schedule, and
shortening length of therapy. In one embodiment, less aggressive
therapy comprises selecting and administering a single therapy
instead of a dual therapy, decreasing drug dosage, decreasing dose
schedule, and shortening length of therapy. In one embodiment, less
aggressive therapy comprises selecting and administering a single
therapy instead of a dual therapy, selecting and administering less
potent drugs, decreasing drug dosage, decreasing dose schedule, and
shortening length of therapy. In one embodiment a less aggressive
therapy comprises selecting and administering a single therapy
instead of a dual therapy.
[0176] In one embodiment a less aggressive therapy comprises
selecting and administering a dual therapy instead of a triple
therapy. In one embodiment a less aggressive therapy comprises
selecting and administering a dual therapy instead of a triple
therapy and delaying administration of anti-HIV disease drugs. In
one embodiment a less aggressive therapy comprises selecting and
administering a dual therapy instead of a triple therapy and
selecting and administering less potent drugs. In one embodiment a
less aggressive therapy comprises selecting and administering a
dual therapy instead of a triple therapy and decreasing dosage of
anti-HIV disease drugs. In one embodiment a less aggressive therapy
comprises selecting and administering a dual therapy instead of a
triple therapy and decreasing the frequency of the dose schedule.
In one embodiment a less aggressive therapy comprises selecting and
administering a dual therapy instead of a triple therapy and
shortening length of therapy. In one embodiment, less aggressive
therapy comprises selecting and administering a dual therapy
instead of a triple therapy, selecting and administering less
potent drugs and decreasing drug dosage. In one embodiment, less
aggressive therapy comprises selecting and administering a dual
therapy instead of a triple therapy, selecting and administering
less potent drugs and decreasing dose schedule. In one embodiment,
less aggressive therapy comprises selecting and administering a
dual therapy instead of a triple therapy, selecting and
administering less potent drugs and shortening length of therapy.
In one embodiment, less aggressive therapy comprises selecting and
administering a dual therapy instead of a triple therapy,
decreasing drug dosage and decreasing dose schedule. In one
embodiment, less aggressive therapy comprises selecting and
administering a dual therapy instead of a triple therapy,
decreasing drug dosage and shortening length of therapy. In one
embodiment, less aggressive therapy comprises selecting and
administering a dual therapy instead of a triple therapy,
decreasing dose schedule and shortening length of therapy. In one
embodiment, less aggressive therapy comprises selecting and
administering a dual therapy instead of a triple therapy, selecting
and administering less potent drugs, decreasing drug dosage, and
decreasing dose schedule. In one embodiment, less aggressive
therapy comprises selecting and administering a dual therapy
instead of a triple therapy, selecting and administering less
potent drugs, decreasing drug dosage, and shortening length of
therapy. In one embodiment, less aggressive therapy comprises
selecting and administering a dual therapy instead of a triple
therapy, selecting and administering less potent drugs, decreasing
dose schedule, and shortening length of therapy. In one embodiment,
less aggressive therapy comprises selecting and administering a
dual therapy instead of a triple therapy, decreasing drug dosage,
decreasing dose schedule, and shortening length of therapy. In one
embodiment, less aggressive therapy comprises selecting and
administering a dual therapy instead of a triple therapy, selecting
and administering less potent drugs, decreasing drug dosage,
decreasing dose schedule, and shortening length of therapy.
[0177] In one aspect of the present application where there is an
increased level of level of sIP-10 or ratio of sIP-10 to total
IP-10 or activity of DPPIV with respect to a reference level,
treatment comprises a more aggressive therapy than a reference
therapy. In one embodiment a more aggressive therapy comprises
earlier administration of anti-HIV disease drugs. In one embodiment
a more aggressive therapy comprises increased dosage of anti-HIV
disease drugs. In one embodiment a more aggressive therapy
comprises increased length of therapy. In one embodiment a more
aggressive therapy comprises increased frequency of the dose
schedule. In one embodiment, more aggressive therapy comprises
selecting and administering more potent drugs and increasing drug
dosage. In one embodiment, more aggressive therapy comprises
selecting and administering more potent drugs and increasing dose
schedule. In one embodiment, more aggressive therapy comprises
selecting and administering more potent drugs and increasing length
of therapy. In one embodiment, more aggressive therapy comprises
increasing drug dosage and increasing dose schedule. In one
embodiment, more aggressive therapy comprises increasing drug
dosage and increasing length of therapy. In one embodiment, more
aggressive therapy comprises increasing dose schedule and
increasing length of therapy. In one embodiment, more aggressive
therapy comprises selecting and administering more potent drugs,
increasing drug dosage, and increasing dose schedule. In one
embodiment, more aggressive therapy comprises selecting and
administering more potent drugs, increasing drug dosage, and
increasing length of therapy. In one embodiment, more aggressive
therapy comprises selecting and administering more potent drugs,
increasing dose schedule, and increasing length of therapy. In one
embodiment, more aggressive therapy comprises increasing drug
dosage, increasing dose schedule, and increasing length of therapy.
In one embodiment, more aggressive therapy comprises selecting and
administering more potent drugs, increasing drug dosage, increasing
dose schedule, and increasing length of therapy.
[0178] In one embodiment a less aggressive therapy comprises
selecting and administering a dual therapy instead of a single
therapy. In one embodiment a more aggressive therapy comprises
selecting and administering a dual therapy instead of a single
therapy and earlier administration of anti-HIV disease drugs. In
one embodiment a more aggressive therapy comprises selecting and
administering a dual therapy instead of a single therapy and
increased dosage of anti-HIV disease drugs. In one embodiment a
more aggressive therapy comprises selecting and administering a
dual therapy instead of a single therapy and increased length of
therapy. In one embodiment a more aggressive therapy comprises
selecting and administering a dual therapy instead of a single
therapy and increased frequency of the dose schedule. In one
embodiment, more aggressive therapy comprises selecting and
administering a dual therapy instead of a single therapy, selecting
and administering more potent drugs and increasing drug dosage. In
one embodiment, more aggressive therapy comprises selecting and
administering a dual therapy instead of a single therapy, selecting
and administering more potent drugs and increasing dose schedule.
In one embodiment, more aggressive therapy comprises selecting and
administering a dual therapy instead of a single therapy, selecting
and administering more potent drugs and increasing length of
therapy. In one embodiment, more aggressive therapy comprises
selecting and administering a dual therapy instead of a single
therapy, increasing drug dosage and increasing dose schedule. In
one embodiment, more aggressive therapy comprises selecting and
administering a dual therapy instead of a single therapy,
increasing drug dosage and increasing length of therapy. In one
embodiment, more aggressive therapy comprises selecting and
administering a dual therapy instead of a single therapy,
increasing dose schedule and increasing length of therapy. In one
embodiment, more aggressive therapy comprises selecting and
administering a dual therapy instead of a single therapy, selecting
and administering more potent drugs, increasing drug dosage, and
increasing dose schedule. In one embodiment, more aggressive
therapy comprises selecting and administering a dual therapy
instead of a single therapy, selecting and administering more
potent drugs, increasing drug dosage, and increasing length of
therapy. In one embodiment, more aggressive therapy comprises
selecting and administering a dual therapy instead of a single
therapy, selecting and administering more potent drugs, increasing
dose schedule, and increasing length of therapy. In one embodiment,
more aggressive therapy comprises selecting and administering a
dual therapy instead of a single therapy, increasing drug dosage,
increasing dose schedule, and increasing length of therapy. In one
embodiment, more aggressive therapy comprises selecting and
administering a dual therapy instead of a single therapy, selecting
and administering more potent drugs, increasing drug dosage,
increasing dose schedule, and increasing length of therapy.
[0179] In one embodiment a more aggressive therapy comprises
selecting and administering a triple therapy instead of a dual
therapy. In one embodiment a more aggressive therapy comprises
selecting and administering a triple therapy instead of a dual
therapy and earlier administration of anti-HIV disease drugs. In
one embodiment a more aggressive therapy comprises selecting and
administering a triple therapy instead of a dual therapy and
increased dosage of anti-HIV disease drugs. In one embodiment a
more aggressive therapy comprises selecting and administering a
triple therapy instead of a dual therapy and increased length of
therapy. In one embodiment a more aggressive therapy comprises
selecting and administering a triple therapy instead of a dual
therapy and increased frequency of the dose schedule. In one
embodiment, more aggressive therapy comprises selecting and
administering a triple therapy instead of a dual therapy, selecting
and administering more potent drugs and increasing drug dosage. In
one embodiment, more aggressive therapy comprises selecting and
administering a triple therapy instead of a dual therapy, selecting
and administering more potent drugs and increasing dose schedule.
In one embodiment, more aggressive therapy comprises selecting and
administering a triple therapy instead of a dual therapy, selecting
and administering more potent drugs and increasing length of
therapy. In one embodiment, more aggressive therapy comprises
selecting and administering a triple therapy instead of a dual
therapy, increasing drug dosage and increasing dose schedule. In
one embodiment, more aggressive therapy comprises selecting and
administering a triple therapy instead of a dual therapy,
increasing drug dosage and increasing length of therapy. In one
embodiment, more aggressive therapy comprises selecting and
administering a triple therapy instead of a dual therapy,
increasing dose schedule and increasing length of therapy. In one
embodiment, more aggressive therapy comprises selecting and
administering a triple therapy instead of a dual therapy, selecting
and administering more potent drugs, increasing drug dosage, and
increasing dose schedule. In one embodiment, more aggressive
therapy comprises selecting and administering a triple therapy
instead of a dual therapy, selecting and administering more potent
drugs, increasing drug dosage, and increasing length of therapy. In
one embodiment, more aggressive therapy comprises selecting and
administering a triple therapy instead of a dual therapy, selecting
and administering more potent drugs, increasing dose schedule, and
increasing length of therapy. In one embodiment, more aggressive
therapy comprises selecting and administering a triple therapy
instead of a dual therapy, increasing drug dosage, increasing dose
schedule, and increasing length of therapy. In one embodiment, more
aggressive therapy comprises selecting and administering a triple
therapy instead of a dual therapy, selecting and administering more
potent drugs, increasing drug dosage, increasing dose schedule, and
increasing length of therapy.
[0180] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention pertains.
Although methods and materials similar or equivalent to those
described herein can be used in the practice or testing of the
present invention, suitable methods and materials are described
below. In case of conflict, the present specification, including
definitions, will control. In addition, the materials, methods, and
examples are illustrative only and not intended to be limiting.
Other features and advantages of the invention will be apparent
from the following detailed description, and from the claims.
EXAMPLES
Total IP-10 Expression is Rapidly Controlled During Non-Pathogenic
SIV Infection
[0181] We searched for factors involved in the lack of chronic
immune activation in the AGM animal model. We showed that AGM,
during acute SIV infection, display signs of inflammation. For
instance, AGM produce IFN-.alpha. and IFN-.gamma. upon SIVagm
infection. However this inflammation is only observed during the
first weeks post-infection and does not persist (Kornfeld et al., J
Clin Invest., 115(4): 1082-1091, 2005; Ploquin et al.,
Retrovirology, 3: 37, 2006; Diop et al., J Virol., 82(11):
5145-5152, 2008). Our data therefore revealed that AGM do not lack
but rather regulate inflammation.
[0182] The capacity of natural hosts to mount an inflammation
during acute infection was highly disputed in the literature. In
order to further demonstrate that AGM do not lack the capacity to
sensor SIVagm infection and mount an innate immune response, we
performed a trancriptome analysis. Among other genes, we measured
the expression profiles of Interferon-stimulated genes (ISG), which
are considered as surrogate markers for IFN activity. We and others
demonstrated a rapid and strong induction of ISGs, including IP-10
(Jacquelin et al., J Clin Invest, 119(12): 3544-3555, 2009; Favre
et al., PLoS Pathog., 5(2): e1000295, 2009). Interestingly, in
contrast to pathogenic SIVmac infection in macaques, the expression
of IP-10 was transient in AGM, in contrast to macaques, where IP-10
expression remains highly elevated (Jacquelin et al., J Clin
Invest, 119(12): 3544-3555, 2009; Favre et al., PLoS Pathog., 5(2):
e1000295, 2009) (FIG. 1).
Plasma Total IP-10 Levels During Acute HIV-1 Infection are Stronger
Predictors of Disease Progression than Viremia and CD4.sup.+ T Cell
Counts
[0183] The data on the differences between pathogenic and
non-pathogenic SIV infection has lead us raise the hypothesis that
uncontrolled inflammation and IFN response at the end of acute HIV
infection could be of bad prognosis for disease progression in
HIV-infected individuals. The concentrations of 28 plasma proteins,
including IFN-I inducible proteins and anti-inflammatory cytokines,
were quantified during acute HIV-1 infection of 133 non-treated
patients. This was a retrospective study, and the disease
progression profiles of each patient were known (Liovat et al.,
Keystone Symposium on HIV Evolution, Genomics and Pathogenesis.
Whistler, Canada; 2011; Liovat et al., 6th IAS Conference on HIV
pathogenesis, treatment and prevention. Rome; 2011; Liovat et al.,
PLoS One, 7(10): e46143, 2012). This study revealed for the first
time an association between inflammation in acute infection and T
cell activation at set-point (i.e. 6 months post-infection).
Moreover, IP-10 was an independent predictor of rapid disease
progression. Of note, when measured in acute HIV-1 infection, IP-10
robustness of prediction was stronger than that of viremia or
CD4.sup.+ T cell counts.
[0184] Only two other studies had analysed before the predictive
capacity of inflammatory molecules during acute HIV infection to
predict subsequent disease progression. Roberts et al did not
identify an association of IP-10 with disease progression (Roberts
et al., Aids, 24(6): 819-31, 2010), while Jiao showed a predictive
value of early IP-10 levels for CD4.sup.+ T cell loss in a cohort
of Chinese patients (Jiao et al., Viral Immunol., 25(4): 333-337,
2012). Other studies had evaluated IP-10 in chronic phase of
infection or after treatment and had a found a negative correlation
with CD4.sup.+ T cell counts and a strong association with viremia
levels (Kamat et al., PLoS One, 7(2): e30881, 2012; Keating et al.,
Aids, 25(15): 1823-32, 2011). Our data indicate for the first time
that when measured in acute HIV-1 infection, IP-10 robustness of
prediction is stronger than that of VL and CD4.sup.+ T cell counts
(Liovat et al., PLoS One, 7(10): e46143, 2012) (FIG. 2).
The Plasma IP-10 Level During Acute HIV-1 Infection is a Stronger
Predictor of Disease Progression than the Viral Reservoir Size
[0185] In order to further demonstrate the robustness of prediction
of IP-10, we wanted to compare it to other markers that have been
associated with disease progression. We already compared it above
to viral RNA levels in plasma. In recent times, numerous studies
stressed the importance of the viral DNA levels, which are
associated with the number of infected cells. Indeed, the viral DNA
copy numbers correspond to the so-called viral reservoir. The size
of this viral reservoir reflects the host's capacity to control
viral replication, infection and spread. The size of the viral
reservoir is remarkably low in HIV controllers and in
post-treatment controllers. It has been suggested that an
early/immediate start of HAART after HIV infection is of benefit
for the patients because it might limit the viral reservoir. A
study carried out on 22 patients enrolled during acute HIV
infection, showed that after several months of HAART, among 22
analytes measured, only IP-10 differed significantly between
treated and non-treated participants (Gay et al., PLoS One, 6(5):
e19617, 2011).
[0186] We are currently collaborating with Pr. Christine Rouzioux
(Hopital Necker). Her team had quantified the viral DNA load in the
same patients, where we had quantified total IP-10 levels. The
levels of IP-10 and viral DNA in acute infection were correlated
(R=0.35 p=0.0001). In multivariate analyses, the plasma levels of
IP-10 during acute infection remained highly predictive of rapid
progression towards AIDS (p=0.003), while viral DNA levels were not
(p=0.47). This supports our previous findings on IP-10 being a
robust and early predictor of disease progression (FIG. 2).
The Plasma IP-10 Level Before HIV-1 Infection Predicts the Rate of
CD4+ T Cell Loss after Infection
[0187] In order to validate our results in an independent cohort,
we contacted the coordinator of the Amsterdam Cohort studies (ACS)
in Netherlands. The ACS are recognized as one of the oldest and
biggest HIV-1 cohorts. A rare feature is that for hundreds of HIV
patients, blood samples collected before infection are available in
the ACS. We thus quantified IP-10 in plasma at different time
points before and after HIV-1 infection in 136 non-treated
patients. The IP-10 levels before infection correlated with the
levels 6 months after HIV infection (R=0.37 p=0.003). Of note, the
levels of IP-10 within the 25 months before infection were
predictive of rapid disease progression upon HIV-1 infection
(OR=3.18 95%1.06-9.55 p=0.03).
The Ratio of the Antagonist Form of IP-10 (Short IP-10) is
Decreased in Acute HIV-1 Infection in Patients Who Subsequently
Progress Rapidly Towards AIDS
[0188] By measuring total IP-10, as we did above, one cannot
distinguish between distinct IP-10 forms, i.e. short and long
forms. During HCV infection, high levels of plasma IP-10 are
predictive of the failure to respond to peg-IFN-a.sub.2/RBV therapy
(Casrouge et al., J Clin Invest., 121(1): 308-317, 2011).
Investigators in the Albert laboratory demonstrated that these
elevated IP-10 levels are mainly in the short antagonist form. This
increased IP-10 antagonism prevents trafficking of CXCR3+
lymphocytes capable to control HCV replication, to the liver, thus
diminishing HCV control and explains the failure of response to
peg-IFN-a.sub.2/RBV treatment ((Casrouge et al., J Clin Invest.,
121(1): 308-317, 2011; Casrouge et al., Clin Exp Immunol., 167(1):
137-148, 2012). We hypothesized that progressive HIV/SIV infections
are associated with decreased IP-10 antagonism, thus enhancing
CXCR3+ lymphocyte trafficking into lymphoid organs and the gut
mucosa amplifying inflammation during HIV/SIV infection. This model
would be the opposite picture of what has been suggested for HCV
infection, where high levels of IP-10 antagonist form are harmful,
while in HIV infection they would limit inflammation and play a
protective role.
[0189] To address this question we started to evaluate the
concentrations of IP-10 antagonist form in plasma from acutely
HIV-infected individuals (ANRS Primo C06 cohort). Using a
standardized ELISA developed in Matthew Albert's laboratory
consisting of a specific antibody raised against the IP-10
antagonist form (Casrouge et al., J Clin Invest., 121(1): 308-317,
2011), we performed a preliminary evaluation of 53 samples. The
ratio of short versus total IP-10 antagonist was decreased during
acute HIV-1 infection in rapid progressors compared to the other
HIV-infected patients, and also compared to healthy donors
(p<0.01) (FIG. 3).
[0190] There was a trend for a positive correlation (R=0.31
p=0.0575) between short IP-10 in acute infection and the CD4 T-cell
counts at set-point 6 months later (M6). Moreover, the ratios of
short against total IP-10 in acute infection negatively correlated
(R=0.4764 p=0.0494) with CD8 T-cell activation at M6.
The Activity of DPPIV is Reduced During Acute Infection of Rapid
Disease Progressors
[0191] Next, we wondered which factors could be responsible for the
distinct levels of IP-10 among the individuals. The Dipeptidyl
peptidase IV (DPPIV) is known to cleave IP-10 into the short IP-10
form. It has already been shown that DPPIV is decreased in the
blood of patients chronically infected by HIV (Blazquez et al., J
Immunol., 149(9): 3073-3077, 1992; De Pasquale et al., Acta
Haematol., 81(1): 19-21, 1989; Gougeon et al., Res Immunol.,
147(1): 5-8, 1996; Vanham et al., J Acquir Immune Defic Syndr,
6(7): 749-757, 1993). We quantified DPPIV for the first time in
acute HIV-1 infection. Importantly, we evaluated DPPIV in patients
showing three distinct types of disease progression profile: slow
progression, normal progression and rapid progression towards AIDS.
Soluble DPPIV activity was measured in 53 patients of the ANRS
Primo Cohort No 6 and 134 patients of the ACS. The plasma levels of
soluble DPPIV were significantly reduced during acute HIV infection
in both cohorts (FIGS. 3 and 4). The levels were significantly
lower in rapid disease progressors than in normal or slow
progressors. Indeed the levels measured in acute HIV-1 infection
were predictive of rapid disease progression (OR=3.27 95%1.05-10.16
p=0.04). Further, the plasmas levels of soluble DPPIV (measured in
sera samples from the ACS cohort) at 6 months after seroconversion
had predictive value for rapid disease progression (OR=1.88
95%1.03-3.45 p=0.04), The robustness was weaker as observed in the
ANRS cohort might be due to measurements carried out at a later
time point. Thus, our study reveals distinct levels of DPPIV
according to the disease progression profile.
[0192] In line with this, the plasma levels of soluble DPPIV
(measured in plasma samples from the ANRS cohort) at primary HIV
infection correlated negatively with viremia as well as with T cell
activation at set-point ((p=0.003, R=-0.76 and p=0.049, R=-0.42,
respectively).
[0193] Ultimately, these data suggest that decreased levels of
IP-10 antagonist form and sDPPIV activity badly influence the viral
and immunologic set-points. In other words, preserving sDPPIV
activity leading to high levels of IP-10 antagonist would be of
good prognosis for HIV-1 infection.
Higher Inflammation in the Gut of SIV-Infected Macaques is
Associated with Lower Expression of DPPIV
[0194] In order to confirm the link between DPPIV and AIDS
pathogenesis, we initiated a study to address this in simian
models. We sampled gut tissue from SIV-infected MAC (n=6) and AGM
(n=5) at day 65 p.i. This corresponds to an interesting time point
as it is situated shortly after acute infection, when IP-10 levels
are already differently regulated between MAC and AGM (Jacquelin et
al., J Clin Invest, 119(12): 3544-3555, 2009). We harvested
fragments of jejunum, ileum, colon and rectum. We quantified IP-10
gene expression levels in enriched intra-epithelial (IEC) and
CD4.sup.+ cells of each of these compartments. IP-10 was
significantly more expressed in the high intestine than in
colon/rectum. We also detected an over-representation of CXCR3 gene
transcripts in CD4+ cells from the MAC high intestine.
[0195] Equally in accordance with our hypothesis, DPP4 gene
expression was less pronounced in CD4.sup.+ cells from MAC than in
AGM (FIG. 5). There was a significant negative correlation between
DPPIV in CD4.sup.+ and in IEC with IP-10 gene expression in the
CD4.sup.+ compartment of the high intestine (FIG. 5).
[0196] Altogether, lower IP-10 inflammation in the gut was
associated with higher levels of DPPIV.
DPPIV Levels in the Jejunum Correlated with Those in Plasma During
SIV Infection
[0197] The intestine corresponds to the major site of replication
for HIV and SIV. According to the literature, virus-host
interactions in the intestine have a major impact on the outcome of
infection (Douek, Top HIV Med., 15(4): 114-117, 2007). With the
help of the animal model, we addressed the question whether the
levels of IP-10 and DPPIV in the blood are representative of the
respective expression levels in the gut during infection. We
quantified IP-10 and soluble DPPIV activity in the plasma of the
same animals for which we had analyzed the gut tissues. The
activity of soluble DPPIV in the plasma of rapidly progressing
macaques seemed lower than in AGM. IP-10 and DPPIV levels in the
jejunum correlated with their respective levels in plasma (R=0.77,
p=0.03; R=0.79, p=0.009, respectively) (FIG. 6). This is in support
for IP-10 and DPPIV in blood as valuable markers reflecting mucosal
inflammation in addition to their predictive values for rapid
disease progression.
CONCLUSION
[0198] Altogether, this is the first time that DPPIV has been
measured during acute HIV-1 infection. Our studies in the animal
model confirm the link between DPPIV and disease progression. They
indicate furthermore that the levels in the blood reflect ongoing
pathogenic processes in the tissues.
[0199] This is also the first time that the short form of IP-10 has
been quantified during HIV infection. In line with the reduced
levels of DPPIV, those patients with the worst clinical prognosis,
displayed the lowest ratios of short IP-10 as compared to the other
HIV-infected individuals.
Sequence CWU 1
1
4177PRTHomo sapiensmisc_featureIP-10 1Val Pro Leu Ser Arg Thr Val
Arg Cys Thr Cys Ile Ser Ile Ser Asn 1 5 10 15 Gln Pro Val Asn Pro
Arg Ser Leu Glu Lys Leu Glu Ile Ile Pro Ala 20 25 30 Ser Gln Phe
Cys Pro Arg Val Glu Ile Ile Ala Thr Met Lys Lys Lys 35 40 45 Gly
Glu Lys Arg Cys Leu Asn Pro Glu Ser Lys Ala Ile Lys Asn Leu 50 55
60 Leu Lys Ala Val Ser Lys Glu Met Ser Lys Arg Ser Pro 65 70 75
275PRTHomo sapiensmisc_featuresIP-10 2Leu Ser Arg Thr Val Arg Cys
Thr Cys Ile Ser Ile Ser Asn Gln Pro 1 5 10 15 Val Asn Pro Arg Ser
Leu Glu Lys Leu Glu Ile Ile Pro Ala Ser Gln 20 25 30 Phe Cys Pro
Arg Val Glu Ile Ile Ala Thr Met Lys Lys Lys Gly Glu 35 40 45 Lys
Arg Cys Leu Asn Pro Glu Ser Lys Ala Ile Lys Asn Leu Leu Lys 50 55
60 Ala Val Ser Lys Glu Met Ser Lys Arg Ser Pro 65 70 75 3766PRTHomo
sapiensmisc_featurehuman DPPIV protein (Swissprot database
Accession No. P27487) 3Met Lys Thr Pro Trp Lys Val Leu Leu Gly Leu
Leu Gly Ala Ala Ala 1 5 10 15 Leu Val Thr Ile Ile Thr Val Pro Val
Val Leu Leu Asn Lys Gly Thr 20 25 30 Asp Asp Ala Thr Ala Asp Ser
Arg Lys Thr Tyr Thr Leu Thr Asp Tyr 35 40 45 Leu Lys Asn Thr Tyr
Arg Leu Lys Leu Tyr Ser Leu Arg Trp Ile Ser 50 55 60 Asp His Glu
Tyr Leu Tyr Lys Gln Glu Asn Asn Ile Leu Val Phe Asn 65 70 75 80 Ala
Glu Tyr Gly Asn Ser Ser Val Phe Leu Glu Asn Ser Thr Phe Asp 85 90
95 Glu Phe Gly His Ser Ile Asn Asp Tyr Ser Ile Ser Pro Asp Gly Gln
100 105 110 Phe Ile Leu Leu Glu Tyr Asn Tyr Val Lys Gln Trp Arg His
Ser Tyr 115 120 125 Thr Ala Ser Tyr Asp Ile Tyr Asp Leu Asn Lys Arg
Gln Leu Ile Thr 130 135 140 Glu Glu Arg Ile Pro Asn Asn Thr Gln Trp
Val Thr Trp Ser Pro Val 145 150 155 160 Gly His Lys Leu Ala Tyr Val
Trp Asn Asn Asp Ile Tyr Val Lys Ile 165 170 175 Glu Pro Asn Leu Pro
Ser Tyr Arg Ile Thr Trp Thr Gly Lys Glu Asp 180 185 190 Ile Ile Tyr
Asn Gly Ile Thr Asp Trp Val Tyr Glu Glu Glu Val Phe 195 200 205 Ser
Ala Tyr Ser Ala Leu Trp Trp Ser Pro Asn Gly Thr Phe Leu Ala 210 215
220 Tyr Ala Gln Phe Asn Asp Thr Glu Val Pro Leu Ile Glu Tyr Ser Phe
225 230 235 240 Tyr Ser Asp Glu Ser Leu Gln Tyr Pro Lys Thr Val Arg
Val Pro Tyr 245 250 255 Pro Lys Ala Gly Ala Val Asn Pro Thr Val Lys
Phe Phe Val Val Asn 260 265 270 Thr Asp Ser Leu Ser Ser Val Thr Asn
Ala Thr Ser Ile Gln Ile Thr 275 280 285 Ala Pro Ala Ser Met Leu Ile
Gly Asp His Tyr Leu Cys Asp Val Thr 290 295 300 Trp Ala Thr Gln Glu
Arg Ile Ser Leu Gln Trp Leu Arg Arg Ile Gln 305 310 315 320 Asn Tyr
Ser Val Met Asp Ile Cys Asp Tyr Asp Glu Ser Ser Gly Arg 325 330 335
Trp Asn Cys Leu Val Ala Arg Gln His Ile Glu Met Ser Thr Thr Gly 340
345 350 Trp Val Gly Arg Phe Arg Pro Ser Glu Pro His Phe Thr Leu Asp
Gly 355 360 365 Asn Ser Phe Tyr Lys Ile Ile Ser Asn Glu Glu Gly Tyr
Arg His Ile 370 375 380 Cys Tyr Phe Gln Ile Asp Lys Lys Asp Cys Thr
Phe Ile Thr Lys Gly 385 390 395 400 Thr Trp Glu Val Ile Gly Ile Glu
Ala Leu Thr Ser Asp Tyr Leu Tyr 405 410 415 Tyr Ile Ser Asn Glu Tyr
Lys Gly Met Pro Gly Gly Arg Asn Leu Tyr 420 425 430 Lys Ile Gln Leu
Ser Asp Tyr Thr Lys Val Thr Cys Leu Ser Cys Glu 435 440 445 Leu Asn
Pro Glu Arg Cys Gln Tyr Tyr Ser Val Ser Phe Ser Lys Glu 450 455 460
Ala Lys Tyr Tyr Gln Leu Arg Cys Ser Gly Pro Gly Leu Pro Leu Tyr 465
470 475 480 Thr Leu His Ser Ser Val Asn Asp Lys Gly Leu Arg Val Leu
Glu Asp 485 490 495 Asn Ser Ala Leu Asp Lys Met Leu Gln Asn Val Gln
Met Pro Ser Lys 500 505 510 Lys Leu Asp Phe Ile Ile Leu Asn Glu Thr
Lys Phe Trp Tyr Gln Met 515 520 525 Ile Leu Pro Pro His Phe Asp Lys
Ser Lys Lys Tyr Pro Leu Leu Leu 530 535 540 Asp Val Tyr Ala Gly Pro
Cys Ser Gln Lys Ala Asp Thr Val Phe Arg 545 550 555 560 Leu Asn Trp
Ala Thr Tyr Leu Ala Ser Thr Glu Asn Ile Ile Val Ala 565 570 575 Ser
Phe Asp Gly Arg Gly Ser Gly Tyr Gln Gly Asp Lys Ile Met His 580 585
590 Ala Ile Asn Arg Arg Leu Gly Thr Phe Glu Val Glu Asp Gln Ile Glu
595 600 605 Ala Ala Arg Gln Phe Ser Lys Met Gly Phe Val Asp Asn Lys
Arg Ile 610 615 620 Ala Ile Trp Gly Trp Ser Tyr Gly Gly Tyr Val Thr
Ser Met Val Leu 625 630 635 640 Gly Ser Gly Ser Gly Val Phe Lys Cys
Gly Ile Ala Val Ala Pro Val 645 650 655 Ser Arg Trp Glu Tyr Tyr Asp
Ser Val Tyr Thr Glu Arg Tyr Met Gly 660 665 670 Leu Pro Thr Pro Glu
Asp Asn Leu Asp His Tyr Arg Asn Ser Thr Val 675 680 685 Met Ser Arg
Ala Glu Asn Phe Lys Gln Val Glu Tyr Leu Leu Ile His 690 695 700 Gly
Thr Ala Asp Asp Asn Val His Phe Gln Gln Ser Ala Gln Ile Ser 705 710
715 720 Lys Ala Leu Val Asp Val Gly Val Asp Phe Gln Ala Met Trp Tyr
Thr 725 730 735 Asp Glu Asp His Gly Ile Ala Ser Ser Thr Ala His Gln
His Ile Tyr 740 745 750 Thr His Met Ser His Phe Ile Lys Gln Cys Phe
Ser Leu Pro 755 760 765 49PRTArtificial SequenceNH2 terminal of the
full-length IP-10 protein 4Val Pro Leu Ser Arg Thr Val Arg Cys 1
5
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